Citrus Sinensis ID: 005812

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Local Sequence Feature Prediction

Residue Number Marker
--------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------
Protein Sequence
MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAEDIEKTMDNKDGVISGAEKHSSKLLESGKTVKPRKAATLGIDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAADAQCKT
Secondary Structure (PSIPRED)
ccccccccccccEEEEEcccHHHHHHHHHHHcccccccEEEEEEEccccHHHHHHcccccccccHHHHHHHccccccccccccccccHHHccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEcccHHHHHccccccccccccccEEEccHHHHHHHHHHHccccccccEEEEEccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEcccccccccEEEEEEEEccHHHHHHHHHHHccccccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccccccHHHHHcccccHHHHHHHHHHcccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHHcccccccEEEccEEEEEEEccccHHHHHHHHHHHccccccccHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHcccccccccccEEEEEcccccccHHHHHHHHHHHHHHHcccccccEEEEEEEEccccccccccccccEEEEEEEccHHHHHHHHHHHcccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccEEEEEEccHHHHHHHHHHHcccEEccEEEEEEEEcccccHHHHHcccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccHHHHHcccEEEEEcccccccHHHHHHHHHHcccEEEEEEcccHHHHHHcccccccccccEEEEEEccHHHHHHHHHHHcccHccccEEEEEEcccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEccccccccEEEEEEEEccHHHHHHHHHHHccccccccEEEEEEEcccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHcHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHcHHcccccccccccccccccEEEEEEccccccHHHHHHHHHHcccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHccccccccEEEccEEEEEEEcccHHHHHHHHHHcccccccccccEEEEccccEccccHHHccccHHHHHHHHHHHHHHHHHHcccccEEcccEEEEEcccccccHHHHHHHHHHHHHcccccccccEEEEEEEEEccccccccccccccEEEEEEccHHHHHHHHHHHHcccccccccccccHHcccccc
Coil and Loop (DISEMBL)
mvtkkgsnehrgfgyvQFAVMEDANRavemkngtsvggrkiGVKHAMHRASLEQRRSKVTQEVQAEDIEktmdnkdgvisgaeKHSSKLlesgktvkprkaatlgidladkedcsqKQRVARTVIIGGLLNADMAEEVHRLAGSIgtvcsvtyplpkeeleqhglaqegckmDASAVLYTTVKSACASVALLHQKEIKGGTVWArqlggegsktqKWKLIIRNIPFKAKVNEIKdmfspvglvwnvyiphntdtglskgFAFVKFTCKRDAESAIQKfngqkfgkrpiavdwavpkniyssggaaagvqnkgdgnsdsgsdddlgdddaetasddsnssekedlpsnadfdeEVDIARKVLNKLTsttgslpslsddsalvkgnkeqdsdktvnesakvsdvsklnsskskpkslkqtegedelQNTIFIcnlpfdldnEEVKQRFSAFgevvsfvpvlhqvtkrpkgtgflkFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLahdkeidksknetndhrnLYLAkeglilegtpaaegvsdddmsKRQMLHEkkmtklqspnfhvsRTRLVIynlpksmtekGLKKLCIDAVVSRASKQKPVIKQIKFLQSlkkgkvdtkhysrgvafVEFTEHQHALVALRVlnnnpsklfyhhcfdaadaqckt
Flexible Loop (DISEMBL)
mvtkkgsnehrgfgyvQFAVMEDANRAVEMkngtsvggrkigVKHAMHrasleqrrskvtqevqaediektmdnkdgvisgaekhsskllesgktvkprkaatlgidladkedcsqkqRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWarqlggegsktqkwkLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAiqkfngqkfgkrpiAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAEtasddsnssekedlpsnadfdEEVDIARKVLNKltsttgslpslsddsalvkgnkeqdsdktvnesakvsdvsklnsskskpkslkqtegedelqNTIFICNLPFDLDNEEVKQRFSAFGEVVsfvpvlhqvtkrpkgtgflKFKTVEAATAAvsaskttsglgiflkgrQLTVLKALDKKlahdkeidksknetndhrnlYLAKeglilegtpaaegvsdddMSKRQMLHEkkmtklqspnfhvsrTRLVIynlpksmtekGLKKLCIDAVVsraskqkpvikqikflqslkkgkvdtKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAADAQCKT
Low Complexity Region (SEG)
MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAEDIEKTMDNKDGVISGAEKHSSKLLESGKTVKPRKAATLGIDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKgdgnsdsgsdddlgdddaetasddsnsseKEDLPSNADFDEEVDIARKVLNKltsttgslpslsddsALVKGNKEQDSDKTVNESAKVSDVsklnsskskpkslkQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFktveaataavsaskttsGLGIFLKGRQLTVlkaldkklahdkEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAADAQCKT
Disordered region (IsUnstruct)
***********GFGYVQFAVMED*********************************************************************************************KQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYS****************************************************************************************************************************QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK*******************LYLAKEGLIL********************************FHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAA******
Disordered Region (DISOPRED)
MVT***SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKH*****************************************************************************TVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLP****************DASAVLYTTVKSACASVALLHQ*************************IIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYS****A****NKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNK*TSTTGSLPSLSDDSAL**********************************************TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKAL*******************************************************************SRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKF*****************VAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAADAQC**
Disordered Region (DISEMBL)
********EHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMH*************EVQAEDIEKTMDNKDGVISGAEKHSSKLLESGKTVKPRKAATLGIDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAG***************************************NADFDEEVDIARKVLNKLTSTTGSLPSLSDDSA******************************************DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAADAQCKT
Disordered Region (DISPRO)
********EHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR******************************************************************QKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGA***********************************************************************************************************************LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEI****NETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKK******HYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHC*D**D**C**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHxxxxxxxxxxxxxxxxxxxxxKTMDNKDGVISGAEKHSSKLLESGKTVKPRKAATLGIDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAADAQCKT
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	676	2.2.26 [Sep-21-2011]
Q8CGC6	750	RNA-binding protein 28 OS	yes	no	0.637	0.574	0.346	2e-48
Q9NW13	759	RNA-binding protein 28 OS	no	no	0.335	0.299	0.448	5e-37
O74400	674	Uncharacterized RNA-bindi	yes	no	0.587	0.589	0.273	1e-26
P37838	685	Nucleolar protein 4 OS=Sa	yes	no	0.332	0.328	0.315	9e-24
P70372	326	ELAV-like protein 1 OS=Mu	no	no	0.258	0.536	0.296	7e-10
Q15717	326	ELAV-like protein 1 OS=Ho	no	no	0.258	0.536	0.291	5e-09
Q6CQR6	878	Multiple RNA-binding doma	no	no	0.346	0.266	0.252	3e-08
Q6GLB5	326	ELAV-like protein 1 OS=Xe	no	no	0.266	0.552	0.276	4e-08
Q5U259	326	ELAV-like protein 1-B OS=	N/A	no	0.264	0.549	0.277	6e-08
Q9Y4C8	960	Probable RNA-binding prot	no	no	0.110	0.078	0.379	7e-08

>sp|Q8CGC6|RBM28_MOUSE RNA-binding protein 28 OS=Mus musculus GN=Rbm28 PE=1 SV=4

 Score =  194 bits (493), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 156/450 (34%), Positives = 235/450 (52%), Gaps = 19/450 (4%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +LIIRN+ FK   +++K +F+  G V  V IP   D G  +GFAFV+F    +A  A++ 
Sbjct: 115 RLIIRNLSFKCSEDDLKAVFTHYGTVLEVNIPKKPD-GKMRGFAFVQFKNLLEAGKALKG 173

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSG--GAAAGVQNKGDGNS-DSGSDD-DLGDDDAETAS 333
            N ++   R +AVDWAV K+ Y      +A GV+   D    +SG  +  + +   ++  
Sbjct: 174 ANMKEIKGRTVAVDWAVAKDKYKDAQHASAPGVKKSSDRKPKESGKKNCRVEEQVEDSDD 233

Query: 334 DDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLS-DDSALVKGNKEQDSDKT 392
           ++ + S  ++    +     V + ++ + +           S +DS L +G    D    
Sbjct: 234 EEDDDSHDDEEERESTIASPVSVHKRAVKRAAPEESIEEDDSYEDSDLEEGGSSYDEGTV 293

Query: 393 VNES-AKVSDVSKLNSSKSKPKSLKQ--TEGEDELQNTIFICNLPFDLDNEEVKQRFSAF 449
            +ES A+  +   +  S+ K + L    TEG+     T+FI NL FD + E + +    F
Sbjct: 294 DSESSAEDQEDEDVPVSEKKKRKLPSDVTEGK-----TVFIRNLSFDSEEEALGEVLQQF 348

Query: 450 GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA-SKTTSGLGIFLKGRQLTVLKAL 508
           G++     VLH  T+  KG  F +F T EAA   ++A S    G G+ L GRQL V  A+
Sbjct: 349 GDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAV 408

Query: 509 DKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKL 568
            +  A   +  K K  T   RNLYLA+EGLI  GT AAEGVS  DM+KR+     K  KL
Sbjct: 409 TRDEAAKLQTKKVKKPTGT-RNLYLAREGLIRAGTKAAEGVSAADMAKRERFELLKHQKL 467

Query: 569 QSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVD 628
           ++ N  VS+TRL ++NLPK++ +K L+KL ++A       +   IK+ + ++ LK     
Sbjct: 468 KNQNIFVSQTRLCLHNLPKAVDDKQLRKLLLEATRGEKGVR---IKECRVMRDLKGVHGK 524

Query: 629 TKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
            K  S G AF EF +H+HAL ALR  NNNP
Sbjct: 525 MKGQSLGYAFAEFQKHEHALRALRHFNNNP 554

Nucleolar component of the spliceosomal ribonucleoprotein complexes.
Mus musculus (taxid: 10090)

>sp|Q9NW13|RBM28_HUMAN RNA-binding protein 28 OS=Homo sapiens GN=RBM28 PE=1 SV=3

 Score =  156 bits (395), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 105/234 (44%), Positives = 138/234 (58%), Gaps = 7/234 (2%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV-S 485
           T+FI NL FD + EE+ +    FGE+     VLH  T+  KG  F +F T EAA   + +
Sbjct: 336 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLA 395

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPA 545
           AS      G+ L GRQL V  A+ +  A   +  K K  T   RNLYLA+EGLI  GT A
Sbjct: 396 ASPENEAGGLKLDGRQLKVDLAVTRDEAAKLQTTKVKKPTGT-RNLYLAREGLIRAGTKA 454

Query: 546 AEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSR 605
           AEGVS  DM+KR+     K  KL+  N  VSRTRL ++NLPK++ +K L+KL + A    
Sbjct: 455 AEGVSAADMAKRERFELLKHQKLKDQNIFVSRTRLCLHNLPKAVDDKQLRKLLLSAT--- 511

Query: 606 ASKQKPV-IKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
            S +K V IK+ + ++ LK    + K  S G AF EF EH+HAL ALR++NNNP
Sbjct: 512 -SGEKGVRIKECRVMRDLKGVHGNMKGQSLGYAFAEFQEHEHALKALRLINNNP 564

Nucleolar component of the spliceosomal ribonucleoprotein complexes.

Homo sapiens (taxid: 9606)

>sp|O74400|YOCE_SCHPO Uncharacterized RNA-binding protein C4F6.14 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC4F6.14 PE=1 SV=1

 Score =  122 bits (305), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 135/494 (27%), Positives = 215/494 (43%), Gaps = 97/494 (19%)

Query: 218 KLIIRNIPFKAK-VNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           +LIIRN+P+  K    ++  FS  G V  + IP     G   GFAFV    ++ AE A+ 
Sbjct: 108 RLIIRNLPWSIKKPQHLEPHFSKFGKVREIKIP-TKGGGRMCGFAFVWMKDRKAAEEAMN 166

Query: 277 KFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDS 336
             NG +   RPIAVDWAV K+ + +               D+ S+    +++ E  SD+ 
Sbjct: 167 SLNGTEIDGRPIAVDWAVSKDAFEATTL-----------KDASSE----EENKEFVSDEG 211

Query: 337 NSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNES 396
           +S   ED  ++++ +EEVD                   S+   L   ++E        E 
Sbjct: 212 HSIVTEDASADSESEEEVD-----------------GHSEGKELAGESEE--------EG 246

Query: 397 AKVSDVSKLNSSKSKPKSLKQTEGEDE-LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSF 455
           + V DV     S S   S+     ++E L++T+F+ NL F+   +E+   F  FG +   
Sbjct: 247 SNVDDVEDSGDSSSDKNSINHEIRDNEGLEDTVFVRNLLFECTEQELYNHFRQFGPLAYA 306

Query: 456 VPVLHQVTKRPKGTGFLKFK-------TVEAATAAVSASKTTS------------GLG-- 494
             V    T R  G GF+KF+        +E A+   +   T +            G+   
Sbjct: 307 KLVKDPATDRSLGRGFIKFRYEKDCQNCLEMASQLPTQEPTEAEKRFLPSVLVDEGIDTD 366

Query: 495 -----IFLKGRQLTVLKALDKKLAHD---KEIDKSKNETN---DHRNLYLAKEGLILEGT 543
                  L GR L V  A+ +K A D   K + + K +     D R+L+L  EG I    
Sbjct: 367 SVSSRFLLHGRLLKVTSAVTRKEASDINQKSLQERKQKMGKGVDRRHLFLLNEGKIAADH 426

Query: 544 PAAEGVSDDDMSKR-QMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAV 602
           P    +S+ D + R Q + ++K    ++P  H+S  RL I N+ + +  K L  L   A+
Sbjct: 427 PLFNSLSETDKTLRSQSIAQRKKLLEKNPTLHLSLNRLSIRNISRHIDPKILAMLGRQAI 486

Query: 603 ------VSRASKQKPV-----------IKQIKFLQSLKKGKVDTKH----YSRGVAFVEF 641
                 VS+  +               +K+ K    LK+ KV+T+      S+G  F++F
Sbjct: 487 RGFMDDVSKGLRANITEEEENLDKGHRLKRGKSGGVLKQAKVETEKAGAGRSKGFGFMQF 546

Query: 642 TEHQHALVALRVLN 655
             H++AL+ALR LN
Sbjct: 547 ISHKYALMALRWLN 560

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

>sp|P37838|NOP4_YEAST Nucleolar protein 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NOP4 PE=1 SV=1

 Score =  112 bits (280), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 91/288 (31%), Positives = 140/288 (48%), Gaps = 63/288 (21%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTV----EAATA 482
           ++F+ N+P+D   E +   FS FG V   +PV+ + T   KGT F+ FK      E    
Sbjct: 291 SVFVRNVPYDATEESLAPHFSKFGSVKYALPVIDKSTGLAKGTAFVAFKDQYTYNECIKN 350

Query: 483 AVSASKTTSGLG------IFLKGRQLTVLKAL---------DKKLAHDKE-IDKSKNETN 526
           A +A  T+  +G         +GR L++   L         +K  A  KE + K+  E  
Sbjct: 351 APAAGSTSLLIGDDVMPEYVYEGRVLSITPTLVREDAGRMAEKNAAKRKEALGKAPGE-K 409

Query: 527 DHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKL-QSPNFHVSRTRLVIYNL 585
           D RNLYL  EG ++EG+  A+ +++ DM  R+  ++ ++ +L ++P+ H+S TRL I NL
Sbjct: 410 DRRNLYLLNEGRVVEGSKMADLLTNTDMEIREKSYKLRVEQLKKNPSLHLSMTRLAIRNL 469

Query: 586 PKSMTEKGLKKLCIDAVVS-------------------RASKQK-----P---------- 611
           P++M +K LK L   AVV                    R++K+K     P          
Sbjct: 470 PRAMNDKALKALARKAVVEFATEVKNKERHPLSKEEIIRSTKEKYKFMGPDEIEAQKKKD 529

Query: 612 ----VIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLN 655
               V+KQ K +  +K     T   SRG  FVEF +H++AL+ LR LN
Sbjct: 530 KKSGVVKQAKVIMEVKGS---TAGRSRGYGFVEFRDHKNALMGLRWLN 574

Required for 60S ribosomal subunit synthesis. Probably involved in the processing of 27S rRNA to produce mature 25S rRNA.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|P70372|ELAV1_MOUSE ELAV-like protein 1 OS=Mus musculus GN=Elavl1 PE=1 SV=2

 Score = 66.6 bits (161), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 56/189 (29%), Positives = 86/189 (45%), Gaps = 14/189 (7%)

Query: 112 EDCSQKQRVARTVIIGGLLNADMA-EEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGC 170
           EDC  +  + RT +I   L  +M  EE+  L  SIG V S    L ++++  H L     
Sbjct: 11  EDC--RDDIGRTNLIVNYLPQNMTQEELRSLFSSIGEVESAK--LIRDKVAGHSLGY--- 63

Query: 171 KMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKV 230
                 V Y T K A  +++ L+   ++  T+            +   L I  +P     
Sbjct: 64  ----GFVNYVTAKDAERAISTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQ 119

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK--FGKRPI 288
            +++DMFS  G + N  +  +  TGLS+G AF++F  + +AE AI  FNG K      PI
Sbjct: 120 KDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPI 179

Query: 289 AVDWAVPKN 297
            V +A   N
Sbjct: 180 TVKFAANPN 188

Binds avidly to the AU-rich element in FOS and IL3/interleukin-3 mRNAs. In the case of the FOS AU-rich element, HUR binds to a core element of 27 nucleotides that contain AUUUA, AUUUUA, and AUUUUUA motifs. Binds preferentially to the 5'-UUUU[AG]UUU-3' motif in vitro.

Mus musculus (taxid: 10090)

>sp|Q15717|ELAV1_HUMAN ELAV-like protein 1 OS=Homo sapiens GN=ELAVL1 PE=1 SV=2

 Score = 63.5 bits (153), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 55/189 (29%), Positives = 85/189 (44%), Gaps = 14/189 (7%)

Query: 112 EDCSQKQRVARTVIIGGLLNADMAE-EVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGC 170
           EDC  +  + RT +I   L  +M + E+  L  SIG V S    L ++++  H L     
Sbjct: 11  EDC--RGDIGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAK--LIRDKVAGHSLGY--- 63

Query: 171 KMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKV 230
                 V Y T K A  ++  L+   ++  T+            +   L I  +P     
Sbjct: 64  ----GFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQ 119

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK--FGKRPI 288
            +++DMFS  G + N  +  +  TGLS+G AF++F  + +AE AI  FNG K      PI
Sbjct: 120 KDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPI 179

Query: 289 AVDWAVPKN 297
            V +A   N
Sbjct: 180 TVKFAANPN 188

Involved in 3'-UTR ARE-mediated MYC stabilization. Binds avidly to the AU-rich element in FOS and IL3/interleukin-3 mRNAs. In the case of the FOS AU-rich element, HUR binds to a core element of 27 nucleotides that contain AUUUA, AUUUUA and AUUUUUA motifs. Binds preferentially to the 5'-UUUU[AG]UUU-3' motif in vitro.

Homo sapiens (taxid: 9606)

>sp|Q6CQR6|MRD1_KLULA Multiple RNA-binding domain-containing protein 1 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=MRD1 PE=3 SV=1

 Score = 61.2 bits (147), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 69/273 (25%), Positives = 120/273 (43%), Gaps = 39/273 (14%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L +RNI + A  ++ + +FSP G +  V+I  +T TG SKGFA+V F    +A +A  +
Sbjct: 331 RLFLRNILYTATEDDFRKLFSPYGELEEVHIAVDTRTGQSKGFAYVLFKNADNAATAFVE 390

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSN 337
            + Q F  R + +   +P +   S               D     +L           +N
Sbjct: 391 LDKQIFQGRLLHI---LPADAKKSHKL------------DEFDLKNLPLKKQRELKRKAN 435

Query: 338 SSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESA 397
           S++ +    N+ +  +  +   V +KL      L    + S+ VK        + + E++
Sbjct: 436 SAQ-QTFSWNSLYMNQDAVLSSVADKLGMKKSELIDAENSSSAVK--------QALAEAS 486

Query: 398 KVSDVSKLNSSK----SKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVV 453
            + DV K   ++    +K   LK +E +D +   I + N P+    EE+ + F  FG+  
Sbjct: 487 VIGDVRKFFETRGVDLTKFAQLKNSERDDRV---ILVKNFPYGTTREEIAELFLPFGK-- 541

Query: 454 SFVPVLHQVTKRPKGT-GFLKFKTVEAATAAVS 485
                L ++   P GT   L+F+ V AA AA S
Sbjct: 542 -----LQRLLLPPSGTIAILQFRDVPAARAAFS 569

Involved in pre-rRNA processing.

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid: 284590)

>sp|Q6GLB5|ELAV1_XENTR ELAV-like protein 1 OS=Xenopus tropicalis GN=elavl1 PE=2 SV=1

 Score = 60.5 bits (145), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 53/192 (27%), Positives = 83/192 (43%), Gaps = 12/192 (6%)

Query: 109 ADKEDCSQKQRVARTVIIGGLLNADMAE-EVHRLAGSIGTVCSVTYPLPKEELEQHGLAQ 167
            D  D   +  + RT +I   L  +M + E+  L  SIG V S    L ++++  H L  
Sbjct: 6   GDHMDDVCRDDIGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAK--LIRDKVAGHSLGY 63

Query: 168 EGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFK 227
                    V Y   K A  ++  L+   ++  T+            +   L I  +P  
Sbjct: 64  -------GFVNYLNAKDAERAINTLNGLRLQSKTIKVSVARPSSESIKDANLYISGLPRT 116

Query: 228 AKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK--FGK 285
               +++DMF P G + N  +  +  TGLS+G AF++F  + +AE AI  FNG K     
Sbjct: 117 MTQKDVEDMFLPFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAIASFNGHKPPGSS 176

Query: 286 RPIAVDWAVPKN 297
            PI V +A   N
Sbjct: 177 EPITVKFAANPN 188

Binds to poly-U elements and AU-rich elements (AREs) in the 3'-UTR of target mRNAs. May be involved in cytoplasmic mRNA polyadenylation. Acts cooperatively with cribp to stabilize AU-rich sequence (ARE)-containing mRNAs. May play a role during gastrulation. Required for the vegetal localization of vg1 mRNA.

Xenopus tropicalis (taxid: 8364)

>sp|Q5U259|ELV1B_XENLA ELAV-like protein 1-B OS=Xenopus laevis GN=elavl1-b PE=1 SV=1

 Score = 60.1 bits (144), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 53/191 (27%), Positives = 83/191 (43%), Gaps = 12/191 (6%)

Query: 110 DKEDCSQKQRVARTVIIGGLLNADMAE-EVHRLAGSIGTVCSVTYPLPKEELEQHGLAQE 168
           D  D   +  + RT +I   L  +M + E+  L  SIG V S    L ++++  H L   
Sbjct: 7   DHMDDVCRDDIGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAK--LIRDKVAGHSLGY- 63

Query: 169 GCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKA 228
                   V Y   K A  ++  L+   ++  T+            +   L I  +P   
Sbjct: 64  ------GFVNYLNAKDAERAINTLNGLRLQSKTIKVSFARPSSETIKDANLYISGLPRTM 117

Query: 229 KVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK--FGKR 286
              +++DMF P G + N  +  +  TGLS+G AF++F  + +AE AI  FNG K      
Sbjct: 118 TQKDVEDMFLPFGHIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAIASFNGHKPPGSSE 177

Query: 287 PIAVDWAVPKN 297
           PI V +A   N
Sbjct: 178 PITVKFAANPN 188

Binds to poly-U elements and AU-rich elements (AREs) in the 3'-UTR of target mRNAs. May be involved in cytoplasmic mRNA polyadenylation. Acts cooperatively with cribp to stabilize AU-rich sequence (ARE)-containing mRNAs. May play a role during gastrulation. Required for the vegetal localization of vg1 mRNA.

Xenopus laevis (taxid: 8355)

>sp|Q9Y4C8|RBM19_HUMAN Probable RNA-binding protein 19 OS=Homo sapiens GN=RBM19 PE=1 SV=3

 Score = 59.7 bits (143), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 48/79 (60%), Gaps = 4/79 (5%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHN-TDTGLSKGFAFVKFTCKRDAESAIQ 276
           K+++RNIPF+A   EI+++FS  G +  V +P   T TG  +GF FV F  K+DA+ A  
Sbjct: 833 KILVRNIPFQAHSREIRELFSTFGELKTVRLPKKMTGTGTHRGFGFVDFLTKQDAKRAFN 892

Query: 277 KF--NGQKFGKRPIAVDWA 293
               +   +G+R + ++WA
Sbjct: 893 ALCHSTHLYGRR-LVLEWA 910

Plays a role in embryo pre-implantation development.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	676
224105333	974	predicted protein [Populus trichocarpa]	0.968	0.672	0.655	0.0
297744765	918	unnamed protein product [Vitis vinifera]	0.977	0.720	0.672	0.0
225427688	972	PREDICTED: uncharacterized protein LOC10	0.983	0.684	0.660	0.0
356546384	956	PREDICTED: RNA-binding protein 28-like [	0.982	0.694	0.647	0.0
356542361	958	PREDICTED: RNA-binding protein 28-like [	0.977	0.689	0.629	0.0
449461647	966	PREDICTED: RNA-binding protein 28-like [	0.968	0.678	0.619	0.0
357441411	962	Eukaryotic translation initiation factor	0.968	0.680	0.612	0.0
297824993	988	RNA recognition motif-containing protein	0.973	0.665	0.544	0.0
255543791	916	RNA-binding protein, putative [Ricinus c	0.906	0.669	0.595	0.0
18399701	1003	RNA recognition motif-containing protein	0.968	0.653	0.525	0.0

>gi|224105333|ref|XP_002313773.1| predicted protein [Populus trichocarpa] gi|222850181|gb|EEE87728.1| predicted protein [Populus trichocarpa]

 Score =  875 bits (2262), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 463/706 (65%), Positives = 540/706 (76%), Gaps = 51/706 (7%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
           MVT+KGS EHRGFG+VQFA+ +DANRA+E+KNG+SVGGRKI VKHAMHRASLEQRR+K  
Sbjct: 50  MVTQKGSTEHRGFGFVQFALKDDANRAIEIKNGSSVGGRKIAVKHAMHRASLEQRRAKAA 109

Query: 61  Q---EVQAEDIEKTMDNKDGVISGAEKHSSKLLESG------------KTVKPRKAATLG 105
           Q   +VQ +D  KT+D K  V S  EKH   +LESG            K  +PRK A L 
Sbjct: 110 QGQGQVQ-DDATKTIDEKGSVASKPEKHVLNVLESGWELWYILSCMLRKPREPRKPAKLV 168

Query: 106 IDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGL 165
            DL DKE+CS+KQRVARTVI GGLLN  MAE+VH+ A   GTVCSVTYPLPKEEL++HGL
Sbjct: 169 TDLTDKENCSEKQRVARTVIFGGLLNDAMAEDVHQRAKETGTVCSVTYPLPKEELKKHGL 228

Query: 166 AQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIP 225
            Q+GC+  ASAVL+T+VK A +SVA+LHQKEIKGG VWARQLGGEG KTQKWKLIIRN+P
Sbjct: 229 EQDGCRSGASAVLFTSVKEARSSVAMLHQKEIKGGIVWARQLGGEGCKTQKWKLIIRNLP 288

Query: 226 FKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK 285
           FKAK NEIK +F   G VW+V++PHN++TGLSKGFAFVKFTCK+DAE+AIQKFNGQKFGK
Sbjct: 289 FKAKPNEIKGVFESAGCVWDVFVPHNSETGLSKGFAFVKFTCKQDAENAIQKFNGQKFGK 348

Query: 286 RPIAVDWAVPKNIYSSGG----------AAAGVQNKGDGNSDSGSDDD--------LGD- 326
           RPIAVDWAVPK IYSSG           A+AG QN+ D + +    DD        +G  
Sbjct: 349 RPIAVDWAVPKKIYSSGANVSAASEDGNASAGHQNEKDSSCEDSDYDDEDDNDTDVIGKK 408

Query: 327 ---DDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKG 383
              D     S DS+ SEKED+P+  DF++E DIARKVL  L +++  +        L KG
Sbjct: 409 QQHDGVVVTSPDSDLSEKEDMPTEVDFEQEADIARKVLRNLIASSSDV--------LPKG 460

Query: 384 NKEQDS----DKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDN 439
            +E ++     K   ES  +S  S L+S KSKP + K  +GED+LQ T+FI NLPFD+++
Sbjct: 461 IEELETVDVPSKLPGESENLSG-SPLSSGKSKPSNTKHIDGEDDLQRTVFISNLPFDVES 519

Query: 440 EEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG 499
            EVKQRFSAFGEV+SFVPVLHQVTKRP+GTGFLKFKT + ATAAVSA+   SGLGIFLKG
Sbjct: 520 GEVKQRFSAFGEVLSFVPVLHQVTKRPRGTGFLKFKTADGATAAVSAANVASGLGIFLKG 579

Query: 500 RQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQM 559
           RQLTV KALDKK AHDKE +K+K E  DHRNLYLAKEGLILEGTPAAEGVS  DM+KR  
Sbjct: 580 RQLTVFKALDKKSAHDKEKEKTKIEDRDHRNLYLAKEGLILEGTPAAEGVSISDMAKRNR 639

Query: 560 LHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFL 619
           L E+KMTKL+SPNFHVSRTRLV+YNLPKSMTEK LKKL IDAV SRA+KQKPVI+Q+KFL
Sbjct: 640 LQEEKMTKLRSPNFHVSRTRLVVYNLPKSMTEKQLKKLFIDAVTSRATKQKPVIRQMKFL 699

Query: 620 QSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHH 665
           +++KKGKV TK +SRGVAFVEFTEHQHALVALRVLNNNP      H
Sbjct: 700 KNVKKGKVVTKDHSRGVAFVEFTEHQHALVALRVLNNNPETFGPEH 745

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297744765|emb|CBI38027.3| unnamed protein product [Vitis vinifera]

 Score =  864 bits (2233), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 461/686 (67%), Positives = 525/686 (76%), Gaps = 25/686 (3%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
           MVT+KGS EHRGFG+VQFAV EDANRA+E+KNG+S+GGRKIGVK AMHR  LEQRRSK  
Sbjct: 50  MVTQKGSTEHRGFGFVQFAVKEDANRAIELKNGSSIGGRKIGVKLAMHRTPLEQRRSKEN 109

Query: 61  QEVQAEDIEKTMDNKDGVISGAEK-HSSKLLESGKTVKPRKAATLGIDLADKEDCSQKQR 119
           Q+    DI KT   KD      ++ H+S L E  K V+ RKA     D ADK   S+KQR
Sbjct: 110 QD----DIIKTRTEKDSSSEVVKQGHASDLQEIEKHVELRKALKPCTDQADKGSFSEKQR 165

Query: 120 VARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLY 179
           VARTVI GGLLNADMAE VH  A  +GTVCSVTYPLPKEELE HGL+Q+GCK+DASAVLY
Sbjct: 166 VARTVIFGGLLNADMAEVVHLRAREVGTVCSVTYPLPKEELEHHGLSQDGCKIDASAVLY 225

Query: 180 TTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSP 239
           ++VK A ASVA+LHQKEIKGG VWARQLGGEGSKTQKWKLI+RN+PFKAKV EIKD+FS 
Sbjct: 226 SSVKEAHASVAMLHQKEIKGGIVWARQLGGEGSKTQKWKLIVRNLPFKAKVTEIKDIFSS 285

Query: 240 VGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIY 299
            G VW+ +IP N++TGLS+GFAFVKFT K+DAE+AIQKFNG+K GKRPIAVDWAVPK IY
Sbjct: 286 AGFVWDAFIPQNSETGLSRGFAFVKFTSKQDAENAIQKFNGEKIGKRPIAVDWAVPKKIY 345

Query: 300 SSGGAAAGVQNKGDGNSDSGSDDDLGDDDAE----------------TASDDSNSSEKED 343
            +G         G  N   G  D   DD  +                +A DDSN++EKE 
Sbjct: 346 ITGANPVVASEDGQLNGRDGEGDTDSDDLEDDTTDIDNKVPHPQGVGSAPDDSNTTEKEV 405

Query: 344 LPSNADFDEEVDIARKVLNKL--TSTTGSLPSLSDDSALVKGNKEQDS-DKTVNESAKVS 400
           +P+  DF+EE DIARKVL  L  +S  G+LPS S     +  ++  D   KT NES K S
Sbjct: 406 MPTEFDFNEEADIARKVLKNLITSSAKGTLPSSSGGPTDLNFDETIDVLKKTSNESEKAS 465

Query: 401 DVSKL-NSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVL 459
           DV++  NSSKSK  +L+  E ED+LQ TIFI NLPFD+D EEVKQ+FS FGEV SFVPVL
Sbjct: 466 DVTEPENSSKSKLLNLRPIESEDDLQRTIFISNLPFDIDKEEVKQQFSKFGEVQSFVPVL 525

Query: 460 HQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEID 519
           HQVTKRPKGTGFLKF TV AA AAVSA+  TS LGIFLKGRQLT LKALDKK AHDKE+ 
Sbjct: 526 HQVTKRPKGTGFLKFNTVAAADAAVSAANPTSSLGIFLKGRQLTALKALDKKSAHDKELK 585

Query: 520 KSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTR 579
           KSK E  DHRNLYLAKEGLI+EGTPAAEGVS  DMSKR ML  +K TKL+SPNFHVSRTR
Sbjct: 586 KSKPEERDHRNLYLAKEGLIVEGTPAAEGVSASDMSKRHMLARQKDTKLESPNFHVSRTR 645

Query: 580 LVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFV 639
           L+IYNLPKSMTEK +KKLCIDAV SRA+KQKP+IKQIKFL+ +KKGKV TK++SRGVAF+
Sbjct: 646 LIIYNLPKSMTEKEVKKLCIDAVTSRATKQKPMIKQIKFLKDMKKGKVVTKNHSRGVAFI 705

Query: 640 EFTEHQHALVALRVLNNNPSKLFYHH 665
           EFTEHQHALVALRVLNNNP      H
Sbjct: 706 EFTEHQHALVALRVLNNNPETFGPEH 731

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225427688|ref|XP_002274081.1| PREDICTED: uncharacterized protein LOC100257200 [Vitis vinifera]

 Score =  864 bits (2232), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 463/701 (66%), Positives = 528/701 (75%), Gaps = 36/701 (5%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
           MVT+KGS EHRGFG+VQFAV EDANRA+E+KNG+S+GGRKIGVK AMHR  LEQRRSK  
Sbjct: 50  MVTQKGSTEHRGFGFVQFAVKEDANRAIELKNGSSIGGRKIGVKLAMHRTPLEQRRSKEN 109

Query: 61  QEVQAEDIEKTMDNKDGVISGAEK-HSSKLLESG---------------KTVKPRKAATL 104
           Q V ++DI KT   KD      ++ H+S L E G               K V+ RKA   
Sbjct: 110 QAVHSDDIIKTRTEKDSSSEVVKQGHASDLQEIGSMSLIFSSITFKNTEKHVELRKALKP 169

Query: 105 GIDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHG 164
             D ADK   S+KQRVARTVI GGLLNADMAE VH  A  +GTVCSVTYPLPKEELE HG
Sbjct: 170 CTDQADKGSFSEKQRVARTVIFGGLLNADMAEVVHLRAREVGTVCSVTYPLPKEELEHHG 229

Query: 165 LAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNI 224
           L+Q+GCK+DASAVLY++VK A ASVA+LHQKEIKGG VWARQLGGEGSKTQKWKLI+RN+
Sbjct: 230 LSQDGCKIDASAVLYSSVKEAHASVAMLHQKEIKGGIVWARQLGGEGSKTQKWKLIVRNL 289

Query: 225 PFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG 284
           PFKAKV EIKD+FS  G VW+ +IP N++TGLS+GFAFVKFT K+DAE+AIQKFNG+K G
Sbjct: 290 PFKAKVTEIKDIFSSAGFVWDAFIPQNSETGLSRGFAFVKFTSKQDAENAIQKFNGEKIG 349

Query: 285 KRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAE-------------- 330
           KRPIAVDWAVPK IY +G         G  N   G  D   DD  +              
Sbjct: 350 KRPIAVDWAVPKKIYITGANPVVASEDGQLNGRDGEGDTDSDDLEDDTTDIDNKVPHPQG 409

Query: 331 --TASDDSNSSEKEDLPSNADFDEEVDIARKVLNKL--TSTTGSLPSLSDDSALVKGNKE 386
             +A DDSN++EKE +P+  DF+EE DIARKVL  L  +S  G+LPS S     +  ++ 
Sbjct: 410 VGSAPDDSNTTEKEVMPTEFDFNEEADIARKVLKNLITSSAKGTLPSSSGGPTDLNFDET 469

Query: 387 QDS-DKTVNESAKVSDVSKL-NSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQ 444
            D   KT NES K SDV++  NSSKSK  +L+  E ED+LQ TIFI NLPFD+D EEVKQ
Sbjct: 470 IDVLKKTSNESEKASDVTEPENSSKSKLLNLRPIESEDDLQRTIFISNLPFDIDKEEVKQ 529

Query: 445 RFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV 504
           +FS FGEV SFVPVLHQVTKRPKGTGFLKF TV AA AAVSA+  TS LGIFLKGRQLT 
Sbjct: 530 QFSKFGEVQSFVPVLHQVTKRPKGTGFLKFNTVAAADAAVSAANPTSSLGIFLKGRQLTA 589

Query: 505 LKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKK 564
           LKALDKK AHDKE+ KSK E  DHRNLYLAKEGLI+EGTPAAEGVS  DMSKR ML  +K
Sbjct: 590 LKALDKKSAHDKELKKSKPEERDHRNLYLAKEGLIVEGTPAAEGVSASDMSKRHMLARQK 649

Query: 565 MTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKK 624
            TKL+SPNFHVSRTRL+IYNLPKSMTEK +KKLCIDAV SRA+KQKP+IKQIKFL+ +KK
Sbjct: 650 DTKLESPNFHVSRTRLIIYNLPKSMTEKEVKKLCIDAVTSRATKQKPMIKQIKFLKDMKK 709

Query: 625 GKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHH 665
           GKV TK++SRGVAF+EFTEHQHALVALRVLNNNP      H
Sbjct: 710 GKVVTKNHSRGVAFIEFTEHQHALVALRVLNNNPETFGPEH 750

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356546384|ref|XP_003541606.1| PREDICTED: RNA-binding protein 28-like [Glycine max]

 Score =  842 bits (2174), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 446/689 (64%), Positives = 519/689 (75%), Gaps = 25/689 (3%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
           MVT+KGS +HRGFGYVQFAV EDANRA+E+KNGTSV GRKI VKHAM R   E+R+SK  
Sbjct: 49  MVTQKGSAQHRGFGYVQFAVEEDANRAIELKNGTSVEGRKIVVKHAMPRPPREERQSKPN 108

Query: 61  QEVQAEDIEKTMDN-KDGVISGAEKHSS-------KLLESGKTVKPR--KAATLGIDLAD 110
           Q  + +D+ K  D+ +DG  SG+EK+ S       ++ +   T KP   K + L  D+AD
Sbjct: 109 QAGKTDDLTKPKDDDEDGRSSGSEKNVSVSKEEELQVSKQKSTRKPMEIKKSALCDDVAD 168

Query: 111 KEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGC 170
           +  CS+KQRVARTVI GGL+N+DMAEEVH  A  IGTVCS+ YPL  ++LEQHGL Q+GC
Sbjct: 169 EGGCSEKQRVARTVIFGGLINSDMAEEVHSKAKEIGTVCSIKYPLSGKDLEQHGLLQDGC 228

Query: 171 KMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKV 230
            +DASAVLYT+VKSA ASVA LH+KEI GG VWARQLGGEGSKTQKWKLIIRN+PFKAK 
Sbjct: 229 TLDASAVLYTSVKSARASVATLHKKEIGGGNVWARQLGGEGSKTQKWKLIIRNLPFKAKD 288

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
           NEI+DMFS  G VW+V+IP   DTGLSKGFAFVKFTCK+DAE AIQK NG KF KR IAV
Sbjct: 289 NEIRDMFSSAGYVWDVFIPQKPDTGLSKGFAFVKFTCKQDAEKAIQKLNGSKFAKRLIAV 348

Query: 291 DWAVPKNIYSSGGAAAGVQNKGDGN-SDSGS-DDDLGDDDAETA------SDDSNSSEKE 342
           DWAV K I+SS    A    KG  N SD  S DDD   DD  +       +D S++ E+E
Sbjct: 349 DWAVSKKIFSSDTNNALASEKGQKNLSDEDSTDDDFELDDKRSGQGDDSDTDYSSAMEEE 408

Query: 343 DLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTV------NES 396
             P + +FD+E DIA+KVLN L +++    S ++DS L+K NKE  SD+ V      NES
Sbjct: 409 GTPED-NFDKEADIAKKVLNNLLTSSSKGTSANNDSMLIKENKESRSDEIVKDADEKNES 467

Query: 397 AKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFV 456
            KVS VSK   S     S+ +   ED+LQ T+FICNLPF+ DNEEVKQRFS FGEV  FV
Sbjct: 468 GKVSGVSKPEISSRNNLSIPKRTEEDDLQGTVFICNLPFECDNEEVKQRFSGFGEVEYFV 527

Query: 457 PVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDK 516
           PVLHQVTKRP+GTGFLKFKTVEAA  A+S +   SG+GI LKGR L VLKALDKK AHDK
Sbjct: 528 PVLHQVTKRPRGTGFLKFKTVEAANTAISTASAASGMGILLKGRPLKVLKALDKKSAHDK 587

Query: 517 EIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVS 576
           E++K+KNE +DHRNLYLAKEGLILEGT AAEGVS  DM KRQ L +KK TKLQSPNFHVS
Sbjct: 588 ELEKAKNEVHDHRNLYLAKEGLILEGTTAAEGVSASDMLKRQELEKKKKTKLQSPNFHVS 647

Query: 577 RTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGV 636
           RTRL+IYNLPKSM EK LKKLCIDAV+SRA+KQKPVI+QIKFL++ KKG V  + YSRGV
Sbjct: 648 RTRLIIYNLPKSMNEKELKKLCIDAVISRATKQKPVIRQIKFLKNEKKGNVAQERYSRGV 707

Query: 637 AFVEFTEHQHALVALRVLNNNPSKLFYHH 665
           AFVEF+EHQHALVALRVLNNNP      H
Sbjct: 708 AFVEFSEHQHALVALRVLNNNPETFGPEH 736

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356542361|ref|XP_003539635.1| PREDICTED: RNA-binding protein 28-like [Glycine max]

 Score =  833 bits (2153), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 436/693 (62%), Positives = 513/693 (74%), Gaps = 32/693 (4%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
           +VT+KGS +HRGFGYVQFAV EDANRA+E+KNGTSV GRKI VKHAM R   E+R+SK  
Sbjct: 49  IVTQKGSAQHRGFGYVQFAVEEDANRAIELKNGTSVEGRKIVVKHAMPRPPCEERQSKPN 108

Query: 61  QEVQAEDIEKTMDN-KDGVISGAEKHSSKLLESGKTV-------KPR--KAATLGIDLAD 110
           +E + +D+ K  D+ +D  +SGAEK+ S L E    V       KP   K + L  D+ D
Sbjct: 109 KEGKTDDLTKPKDDDEDSTLSGAEKNVSVLKEEEVQVSKQKNMRKPTETKKSALCDDVPD 168

Query: 111 KEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGC 170
           +  CS+KQRVARTVI GGL+N+DMAEEVH  A  IGTVCS+ YPL +++LEQHGL Q+GC
Sbjct: 169 EGSCSEKQRVARTVIFGGLINSDMAEEVHGKAREIGTVCSIKYPLSRKDLEQHGLLQDGC 228

Query: 171 KMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKV 230
            +DASAVLYT+VKSA ASVA LH+KEI GG +W RQLGGEGSKTQKWKLI+RN+PFKAK 
Sbjct: 229 TLDASAVLYTSVKSARASVATLHRKEIGGGNIWVRQLGGEGSKTQKWKLIVRNLPFKAKE 288

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
           NEI+DMFS  G VW+V+IP  T+T LSKGFAFVKFTCK+DAE AIQK NG KF KR IAV
Sbjct: 289 NEIRDMFSSAGCVWDVFIPQKTNTDLSKGFAFVKFTCKQDAEKAIQKLNGSKFAKRLIAV 348

Query: 291 DWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAE----------TASDDSNSSE 340
           DWAV K I+SS    A    KG  N    SD+D  D+D E          + +D S++ E
Sbjct: 349 DWAVSKKIFSSDTNNALASEKGQQNM---SDEDSTDEDFELVDKRSGQGDSDTDYSSAME 405

Query: 341 KEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTV------- 393
           +E  P   +FD+E DIA+KVLN L +++    S+++DS L+K NK   SD+ V       
Sbjct: 406 EEGTPPEDNFDKEADIAKKVLNNLLTSSSKGTSVNNDSMLIKENKGSRSDEIVKDADEKA 465

Query: 394 -NESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEV 452
            NES KVS VSK   S S+   L     ED+LQ T+FI NLPF+ DNEEVKQRFS FGE+
Sbjct: 466 SNESEKVSGVSKPEIS-SRNNLLNPKGTEDDLQRTVFISNLPFECDNEEVKQRFSGFGEI 524

Query: 453 VSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKL 512
             FVPVLHQVTKRP+GTGFLKFKTVEAA   +S ++  SG+GI LKGR L VLKALDKK 
Sbjct: 525 EYFVPVLHQVTKRPRGTGFLKFKTVEAANTVISTARAASGMGILLKGRPLKVLKALDKKS 584

Query: 513 AHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPN 572
           AHDKE++K+KNE +DHRNLYLAKEGLILEGT AAEGVS  DM KR  L  KK TKLQSPN
Sbjct: 585 AHDKELEKAKNEVHDHRNLYLAKEGLILEGTTAAEGVSASDMLKRLELERKKKTKLQSPN 644

Query: 573 FHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHY 632
           FHVSRTRL+IYNLPKSM EK LKK CIDAVVSRA+KQKPVI+QIKFL++ KKG V  + Y
Sbjct: 645 FHVSRTRLIIYNLPKSMNEKELKKFCIDAVVSRATKQKPVIRQIKFLKNEKKGNVAQERY 704

Query: 633 SRGVAFVEFTEHQHALVALRVLNNNPSKLFYHH 665
           SRGVAFVEF+EHQHALVALRVLNNNP      H
Sbjct: 705 SRGVAFVEFSEHQHALVALRVLNNNPETFGPEH 737

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449461647|ref|XP_004148553.1| PREDICTED: RNA-binding protein 28-like [Cucumis sativus]

 Score =  807 bits (2084), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 432/697 (61%), Positives = 514/697 (73%), Gaps = 42/697 (6%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
           MVT+KGS EHRGFG+VQFAV EDANRA+++KNG S  GRKI VKHAMHRA LEQRRSK  
Sbjct: 54  MVTQKGSTEHRGFGFVQFAVAEDANRAIQLKNGLSFEGRKITVKHAMHRAPLEQRRSKEN 113

Query: 61  Q----------EVQAEDIEKTMDNKDGVIS-------GAEKHSSKLLESG--------KT 95
           Q          E     +E+    KD   S         E+ +SK  E          + 
Sbjct: 114 QVAGSTLAANEEGDTSKMEEHPTTKDKGTSKRDVQPINEERDTSKRAEQTISNSEGKERH 173

Query: 96  VKPRKAATLGIDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPL 155
           +  RK A L   L DKE  S KQR+ARTV+IGGLL+ DMAE+VHR    +G VCS+ YPL
Sbjct: 174 LSARKLAPLSSYLEDKEGHSGKQRIARTVVIGGLLDGDMAEDVHRQVRDVGGVCSIVYPL 233

Query: 156 PKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQ 215
           P++E+EQHG+ ++GCKMD SAVL+ +VKSA A+VA+LHQKE+KGG VWARQLGGEGSKTQ
Sbjct: 234 PRKEVEQHGILRDGCKMDVSAVLFDSVKSARAAVAILHQKEMKGGVVWARQLGGEGSKTQ 293

Query: 216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           KWK+I+RN+PFKAK  EIK+ FS  G VW+V +P N+DTGLSKGFAFVKFTCK+DAESAI
Sbjct: 294 KWKVIVRNLPFKAKEKEIKNTFSSAGFVWDVMMPQNSDTGLSKGFAFVKFTCKQDAESAI 353

Query: 276 QKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGN--------SDSGSDDDLGDD 327
           QKFNG+KFG+R IAVDWAVPK IYSSGG A    +  D +        S SGSD    + 
Sbjct: 354 QKFNGKKFGQRTIAVDWAVPKKIYSSGGGATAPVDSDDEDQTERDREGSISGSDSRDENT 413

Query: 328 DAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTG--SLPSLSDDSALVKGNK 385
               +   S  SEKED+ S  DF+ E +IARKVL  L S++   +LPSL+D +   K NK
Sbjct: 414 GHNESESSSEDSEKEDISSEVDFEGETEIARKVLETLISSSAKEALPSLTDGNPPSKVNK 473

Query: 386 EQDSDKTVNESAKVSDVS----KLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEE 441
           E D D +   S     VS    KL  S+SK   LKQT+ ED L+ T++I NLPFD+DNEE
Sbjct: 474 EPDFDSSKKSSDMSDKVSNEPGKL--SESKTSILKQTDEED-LKRTVYIGNLPFDIDNEE 530

Query: 442 VKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ 501
           VKQRFS FGEV+SFVPVLHQVTKRPKGTGFLKFKT +AA  AVS++   SG+GIFLKGRQ
Sbjct: 531 VKQRFSGFGEVLSFVPVLHQVTKRPKGTGFLKFKTADAANVAVSSANAASGVGIFLKGRQ 590

Query: 502 LTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLH 561
           L VL ALDKK A DKE++KSKN+ +DHRNLYLA+EG+ILEGTPAAEGVS  DM KRQ L 
Sbjct: 591 LKVLNALDKKSAQDKELEKSKNDNHDHRNLYLAQEGIILEGTPAAEGVSASDMEKRQRLE 650

Query: 562 EKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQS 621
           +K+ TKLQSPNFHVSRTRLVI+NLPKSM EK L KLCI+AV SRA+KQKPVI+QIKFL+ 
Sbjct: 651 KKRTTKLQSPNFHVSRTRLVIHNLPKSMKEKELHKLCIEAVTSRATKQKPVIRQIKFLKD 710

Query: 622 LKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
           +KKGK+ TK++S GVAF+EF+EH+HALVALRVLNNNP
Sbjct: 711 VKKGKMLTKNHSCGVAFIEFSEHEHALVALRVLNNNP 747

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357441411|ref|XP_003590983.1| Eukaryotic translation initiation factor 3 subunit G [Medicago truncatula] gi|355480031|gb|AES61234.1| Eukaryotic translation initiation factor 3 subunit G [Medicago truncatula]

 Score =  801 bits (2068), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 427/697 (61%), Positives = 510/697 (73%), Gaps = 42/697 (6%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
           MVT+KGS +HRGFGYVQFAV +DAN+A+E+KN + VG RKI VKHA+ R   E RRSK  
Sbjct: 52  MVTQKGSTQHRGFGYVQFAVEKDANQAIELKNSSLVGDRKIVVKHAIPRPPRENRRSKPD 111

Query: 61  QEVQAEDI-EKTMDNKDGVISGAEKHSS----------KLLE----SGKTVKPRKAATLG 105
           QE    D+ E   D+KD  +SGAEK  S          K+L+    S K V+ +KAA L 
Sbjct: 112 QEGNEGDLTESKNDDKDSELSGAEKPVSVPKEPKEEEVKVLDKPKNSRKPVEIKKAA-LC 170

Query: 106 IDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGL 165
            D AD+   S+KQ+VARTVI GGL+N+ MAE+VHR A  IGTVCS+ +PL + +L+QHGL
Sbjct: 171 NDAADEGGGSEKQKVARTVIFGGLVNSAMAEDVHRQAREIGTVCSIKHPLSRNDLQQHGL 230

Query: 166 AQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIP 225
            QEGC  +ASAVLYT+VKSA ASVA LH+KEI GGTVWARQLGGEG+KTQKWKLI+RN+P
Sbjct: 231 LQEGCTFNASAVLYTSVKSARASVATLHKKEIGGGTVWARQLGGEGAKTQKWKLIVRNLP 290

Query: 226 FKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK 285
           FKAK NEI+D FS  G VW V+IP  +DTGLSKGFAFVKFTCK+DAE+AI+K NG KFG 
Sbjct: 291 FKAKENEIRDAFSSAGTVWEVFIPQKSDTGLSKGFAFVKFTCKQDAENAIRKLNGSKFGS 350

Query: 286 RPIAVDWAVPKNIYSSG-----GAAAGVQNKGDGNSDSGSDDDLGDDDAET-ASDDSN-- 337
           R IAVDWAVPK I+SS       +  G Q   D +  + ++DDL + D ++   DDS+  
Sbjct: 351 RLIAVDWAVPKKIFSSDTNDAPASEEGQQKVTDEDGSTTTEDDLENTDKKSDQGDDSDID 410

Query: 338 SSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVN--- 394
           S  +ED+PS  DFD+E DIARKVLN L +++    S+++DS   +   +  S +TV    
Sbjct: 411 SVVEEDVPSEDDFDKEADIARKVLNNLITSSAKDESVNNDSVSSEEKNKPKSKETVKGAD 470

Query: 395 -----ESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAF 449
                ES KVSD+SK  +SK         E ED+L  T+FI NLPF+LD EE+KQRFSAF
Sbjct: 471 SKTSKESDKVSDISKPETSK---------ETEDDLHRTVFITNLPFELDTEELKQRFSAF 521

Query: 450 GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALD 509
           GEV  F PVLHQVTKRP+GTGFLKFKT EAA  A+S + T SG+GI +KGR L VLKALD
Sbjct: 522 GEVEYFAPVLHQVTKRPRGTGFLKFKTAEAADNAISTANTASGMGILVKGRPLKVLKALD 581

Query: 510 KKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQ 569
           KK AHDKE +K KNE  DHRNLYLAKEGLIL+GTPAAEGVS  DMSKR+ L  KK TKLQ
Sbjct: 582 KKSAHDKEQEKEKNEVQDHRNLYLAKEGLILDGTPAAEGVSATDMSKRKNLERKKKTKLQ 641

Query: 570 SPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGK-VD 628
           SPNFHVS+TRLVIYNLPKSMTEK LK LCIDAV+SRA+KQ PVI+QIK L+  +KGK   
Sbjct: 642 SPNFHVSKTRLVIYNLPKSMTEKQLKTLCIDAVISRATKQIPVIRQIKILKDGRKGKATQ 701

Query: 629 TKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHH 665
            + YSRGVAF+EF+EHQHALVALRVLNNNP      H
Sbjct: 702 EQQYSRGVAFLEFSEHQHALVALRVLNNNPETFGPEH 738

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297824993|ref|XP_002880379.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297326218|gb|EFH56638.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  753 bits (1945), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 403/740 (54%), Positives = 503/740 (67%), Gaps = 82/740 (11%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
           ++T KGSNEHRGF +V FA+ ED NRA+E+KNG++ GGR+I VK A +R SL++RR+K  
Sbjct: 51  LITNKGSNEHRGFAFVTFALPEDVNRAIELKNGSTFGGRRITVKQATNRPSLKERRTKAV 110

Query: 61  QEVQAEDIEKTMDNKDGVISGAE----------------KHSSKLLESGKTVKP------ 98
           Q +   D  +   +KD +I   +                K   K +ES K  KP      
Sbjct: 111 QGISLPDDSQAQSDKDTLIPETDEKVPPPETKVEKPIERKKVEKPIESKKVEKPIERKKV 170

Query: 99  -----------------------RKAAT-LGIDLADKEDCSQKQRVARTVIIGGLLNADM 134
                                  RK  T L +DL DKE CS KQRVARTVI GGL NA+M
Sbjct: 171 EKPIESKKVEKPIERKQVEKPIERKGPTKLHVDLPDKETCSDKQRVARTVIFGGLANAEM 230

Query: 135 AEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQ 194
           AE VH     IGTVCSV YPLPKEEL+Q+GL Q+GC+ +ASAVL+T+VKSACA VA LHQ
Sbjct: 231 AEVVHSRVKEIGTVCSVRYPLPKEELQQNGLTQDGCRAEASAVLFTSVKSACAVVAKLHQ 290

Query: 195 KEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDT 254
            EIKG  +WARQLGGEGSK QKWKLIIRN+PF+AK ++IK++FS VG VW+V+IP N +T
Sbjct: 291 TEIKGNLIWARQLGGEGSKAQKWKLIIRNLPFQAKPSDIKEVFSAVGFVWDVFIPKNFET 350

Query: 255 GLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYS-----SGGAAAGVQ 309
           GL KGFAFVKFTCK+DAE+AIQ FNG  FGKRPIAVDWAVPKN+Y+     +  +A G Q
Sbjct: 351 GLPKGFAFVKFTCKKDAENAIQMFNGHMFGKRPIAVDWAVPKNLYNGAADATTASADGDQ 410

Query: 310 NKGDGNSDSGSDDDLGDDDAETAS------------------DDSNSSEKEDLPSNADFD 351
              DG+SD+ S D    DDA  +                    +S++ EK D+ ++ +F 
Sbjct: 411 KGSDGDSDNSSVDLEEVDDAVESHPPSGDDTDDEEEDGSNKLSESDALEK-DVGTDVNFK 469

Query: 352 EEVDIARKVL-NKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAK-VSDVS----KL 405
           EE D+ARKVL N L S+ GS+ S   ++      +E D  K  N S K V+D S     L
Sbjct: 470 EEADVARKVLKNLLASSKGSIASPDGET------EESDKSKLKNSSTKPVADSSGVSEPL 523

Query: 406 NSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKR 465
            S K+K  + K+T+  +  + T+FI N+PFD+  EEVKQ+F+ FGEV S   VL++VTKR
Sbjct: 524 KSGKTKEVAPKETQENEHFERTLFIRNIPFDVTKEEVKQKFAVFGEVESLFLVLNKVTKR 583

Query: 466 PKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNET 525
           P+GT FLKFK  +A+ AA+SA+ T SG+G+ LKGRQL V++A+ KK AHD E+ K++ + 
Sbjct: 584 PEGTAFLKFKKADASVAAISAANTASGVGVLLKGRQLNVMRAVGKKAAHDIELKKTEEKN 643

Query: 526 NDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNL 585
            DHRNLYLAKEG IL+ +PAAEGVS +DM +R+ LHE KM KLQSPNFHVSRTRLVIYNL
Sbjct: 644 VDHRNLYLAKEGQILDDSPAAEGVSAEDMDRRRRLHENKMKKLQSPNFHVSRTRLVIYNL 703

Query: 586 PKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQ 645
           PKSM +K L KL +DAV SRA+KQKP I+QIKFLQ+ KKGKVDTK+YSRGVAFVEFTEH+
Sbjct: 704 PKSMNQKQLHKLLVDAVTSRATKQKPGIRQIKFLQNEKKGKVDTKNYSRGVAFVEFTEHE 763

Query: 646 HALVALRVLNNNPSKLFYHH 665
           HALVALRVLNNNP      H
Sbjct: 764 HALVALRVLNNNPETFGPQH 783

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255543791|ref|XP_002512958.1| RNA-binding protein, putative [Ricinus communis] gi|223547969|gb|EEF49461.1| RNA-binding protein, putative [Ricinus communis]

 Score =  751 bits (1939), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 405/680 (59%), Positives = 495/680 (72%), Gaps = 67/680 (9%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
           +VT+KGS+EHRGFG+VQFA+ EDANRA+E+K+G+SV G+KI VKHAM RA L+QRR+K  
Sbjct: 54  LVTQKGSSEHRGFGFVQFAIKEDANRAIELKDGSSVSGQKIFVKHAMSRAPLDQRRAKAA 113

Query: 61  QEVQAEDIEKTMDNKDGVISGAEKHSSKLLESGKTVKPRKAATLGIDLADKEDCSQKQRV 120
           Q V+++   KT ++   V    +K++SKL E+ K +KPRK   L  +L D+E+CS+KQRV
Sbjct: 114 QVVESDGAAKTENDTTRV----DKYASKLTEAVKHLKPRKPVKLSSELVDEENCSEKQRV 169

Query: 121 ARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYT 180
           ARTVI GGLL+  MAEEVHRLA  +G  CSVTYPLPKE+LE++GLAQ+GC+ D SA+LYT
Sbjct: 170 ARTVIFGGLLDDAMAEEVHRLAREVGNACSVTYPLPKEDLEKNGLAQDGCRSDVSAILYT 229

Query: 181 TVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPV 240
           +VK A  SV +LHQKEI+GG VWARQLGGEGSKTQKWKLI+RN+PFKA            
Sbjct: 230 SVKEARLSVRMLHQKEIRGGIVWARQLGGEGSKTQKWKLIVRNLPFKA------------ 277

Query: 241 GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYS 300
                                             I++FN QK+GKRP+AVDWAV K +YS
Sbjct: 278 ----------------------------------IKQFNLQKYGKRPMAVDWAVSKKMYS 303

Query: 301 SGGAAA-----GVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVD 355
           SG   +     G QN+ DG+SD   DD+  DD  + ASD+S+  EK D+P+  DFD E D
Sbjct: 304 SGAIGSVPPEEGHQNESDGSSDDTEDDENDDD-VDGASDNSDPFEKNDMPTEGDFDAEAD 362

Query: 356 IARKVLNKLT-STTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKS 414
           +ARKVLN +T S+ G+     DDS +  G ++ +SD+TV      S V +  S  + P+ 
Sbjct: 363 MARKVLNSITLSSKGTSTIDVDDSVVPMGTQKPNSDETVILPKSNSSVQENMSGFTVPEK 422

Query: 415 LKQTEG---------EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKR 465
             +++          +D+LQ T+FI NLPFD DNEEVKQRFS FGEV SFVPVLHQVTKR
Sbjct: 423 SGKSDSADVRKAAIDDDDLQRTVFISNLPFDADNEEVKQRFSVFGEVKSFVPVLHQVTKR 482

Query: 466 PKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNET 525
           P+GTGFLKFKT +AA AAVSA+   SGLGI LKGRQLTVLKALDK  AH+KE++K+KNE 
Sbjct: 483 PRGTGFLKFKTEDAAIAAVSAANLASGLGILLKGRQLTVLKALDKNSAHNKEMEKAKNED 542

Query: 526 NDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNL 585
           NDHRNLYLAKEG+ILEGTPA+EGVS  DM KR+ LHEKKMTKL+SPNFHVSR RLV+YNL
Sbjct: 543 NDHRNLYLAKEGVILEGTPASEGVSASDMDKRKALHEKKMTKLRSPNFHVSRNRLVVYNL 602

Query: 586 PKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQ 645
           P S+TEK LKKLCIDAV+SRA+KQKPVI+QIKFLQS K GKV TK++SRGVAF+EFTEHQ
Sbjct: 603 PHSVTEKKLKKLCIDAVISRATKQKPVIRQIKFLQSTKTGKV-TKNHSRGVAFIEFTEHQ 661

Query: 646 HALVALRVLNNNPSKLFYHH 665
           HALVALRVLNNNP      H
Sbjct: 662 HALVALRVLNNNPETFGPEH 681

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18399701|ref|NP_565513.1| RNA recognition motif-containing protein [Arabidopsis thaliana] gi|4567275|gb|AAD23688.1| expressed protein [Arabidopsis thaliana] gi|16604631|gb|AAL24108.1| unknown protein [Arabidopsis thaliana] gi|27754736|gb|AAO22811.1| unknown protein [Arabidopsis thaliana] gi|330252084|gb|AEC07178.1| RNA recognition motif-containing protein [Arabidopsis thaliana]

 Score =  733 bits (1892), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 399/760 (52%), Positives = 496/760 (65%), Gaps = 105/760 (13%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
           +VT KGS+EHRGF +V+FA+ ED NRA+E+KNG++VGGR+I VK A HR SL++RR+K  
Sbjct: 51  LVTNKGSDEHRGFAFVKFALQEDVNRAIELKNGSTVGGRRITVKQAAHRPSLQERRTKAA 110

Query: 61  QEVQAEDIEKTMDNKDGVI-------SGAEKHSSKLLESGKTVKP-----------RKAA 102
           + +   D  +   +KD  I       S  EK   K +E  K  KP           RK A
Sbjct: 111 EGISVPDNSQGQSDKDTSIPETDEKVSPPEKKLEKPVERKKVEKPIERKQVEKPVERKKA 170

Query: 103 TLGID----------------------------------------------LADKEDCSQ 116
              I+                                              L DKE CS 
Sbjct: 171 EKPIELKQVEKPFERKQVEKPVERKQVEKPVERKQVEKPIERKRPTKLHVDLPDKETCSD 230

Query: 117 KQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASA 176
           KQRVARTVI GGL NA+MAE VH     IGTVCSV YPLPKEEL+Q+GL Q+GC+ +ASA
Sbjct: 231 KQRVARTVIFGGLANAEMAEVVHSRVKEIGTVCSVRYPLPKEELQQNGLTQDGCRAEASA 290

Query: 177 VLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDM 236
           VL+T+VKSACA+VA LHQ E+KG  +WARQLGGEGSK QKWKLIIRN+PF+AK ++IK +
Sbjct: 291 VLFTSVKSACAAVAKLHQTEVKGNLIWARQLGGEGSKAQKWKLIIRNLPFQAKPSDIKVV 350

Query: 237 FSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           FS VG VW+V+IP N +TGL KGFAFVKFTCK+DA +AI+KFNG  FGKRPIAVDWAVPK
Sbjct: 351 FSAVGFVWDVFIPKNFETGLPKGFAFVKFTCKKDAANAIKKFNGHMFGKRPIAVDWAVPK 410

Query: 297 NIYSSGGAAAGVQNKGDGNSDSGSDD----DLGDDDAETAS------------------D 334
           NIY+    A      GD     G  +    DL + D    S                   
Sbjct: 411 NIYNGAADATTASADGDKEGSDGDSENSSVDLEEVDEAVESHPPPGDDTDDDEDGSNKLT 470

Query: 335 DSNSSEKEDLPSNADFDEEVDIARKVL-NKLTSTTGSLPSLSDDSALVKGNKEQ------ 387
           +S++ +K D+ ++ +F++E D+ARKVL N L S+ GS       +A  +G  E+      
Sbjct: 471 ESDALDK-DVGTDMNFEDEADVARKVLKNLLASSKGS-------TATPEGETEESDKSKL 522

Query: 388 --DSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQR 445
              S K V +S+ VS+   L S K+K  + K+T+  D+ + T+FI NLPFD+  EEVKQR
Sbjct: 523 KSSSTKPVADSSGVSE--PLKSGKTKVVAPKETQDNDDFERTLFIRNLPFDVTKEEVKQR 580

Query: 446 FSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL 505
           F+ FGEV S   VLH+VTKRP+GT F+KFKT +A+ AA+SA+ T SG+G+ LKGRQL V+
Sbjct: 581 FTVFGEVESLSLVLHKVTKRPEGTAFVKFKTADASVAAISAADTASGVGVLLKGRQLNVM 640

Query: 506 KALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKM 565
           +A+ KK A D E+ K++ +  DHRNLYLAKEG IL+ TPAAEGVS +DM KR+ LHE KM
Sbjct: 641 RAVGKKAAKDIELKKTEEKNVDHRNLYLAKEGQILDDTPAAEGVSAEDMDKRRRLHENKM 700

Query: 566 TKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKG 625
             LQSPNFHVSRTRLVIYNLPKSM  K L +L +DAV SRA+KQKP I+QIKFLQ+ KKG
Sbjct: 701 KMLQSPNFHVSRTRLVIYNLPKSMNPKQLNRLLVDAVTSRATKQKPCIRQIKFLQNEKKG 760

Query: 626 KVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHH 665
           KVDTK+YSRGVAFVEFTEH+HALVALRVLNNNP      H
Sbjct: 761 KVDTKNYSRGVAFVEFTEHEHALVALRVLNNNPETFGPQH 800

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	676
TAIR|locus:2050024	1003	AT2G21440 [Arabidopsis thalian	0.476	0.321	0.518	5.1e-164
UNIPROTKB|Q9NW13	759	RBM28 "RNA-binding protein 28"	0.647	0.577	0.313	8.5e-48
UNIPROTKB|E1BLD4	756	RBM28 "Uncharacterized protein	0.337	0.301	0.403	1.2e-45
UNIPROTKB|E2RIB8	751	RBM28 "Uncharacterized protein	0.334	0.300	0.412	6.1e-45
ZFIN|ZDB-GENE-040426-960	865	rbm28 "RNA binding motif prote	0.334	0.261	0.376	1.6e-43
RGD|1311336	749	Rbm28 "RNA binding motif prote	0.335	0.303	0.405	5.4e-43
MGI|MGI:2655711	750	Rbm28 "RNA binding motif prote	0.337	0.304	0.399	6e-43
UNIPROTKB|G3MZL2	610	RBM28 "Uncharacterized protein	0.337	0.373	0.403	3e-34
WB|WBGene00011043	608	rbm-28 [Caenorhabditis elegans	0.338	0.376	0.298	1.7e-33
ASPGD|ASPL0000078272	724	AN4330 [Emericella nidulans (t	0.140	0.131	0.357	4e-31

TAIR|locus:2050024 AT2G21440 [Arabidopsis thaliana (taxid:3702)]

 Score = 810 (290.2 bits), Expect = 5.1e-164, Sum P(2) = 5.1e-164
 Identities = 169/326 (51%), Positives = 207/326 (63%)

Query:   342 EDLPSNADFDEEVDIARKVLNKXXXXXXXXXXX--XXXXALVKGNKEQDSDKTVNESAKV 399
             +D+ ++ +F++E D+ARKVL                      K   +  S K V +S+ V
Sbjct:   477 KDVGTDMNFEDEADVARKVLKNLLASSKGSTATPEGETEESDKSKLKSSSTKPVADSSGV 536

Query:   400 SDVXXXXXXXXXXXXXXQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVL 459
             S+               +T+  D+ + T+FI NLPFD+  EEVKQRF+ FGEV S   VL
Sbjct:   537 SEPLKSGKTKVVAPK--ETQDNDDFERTLFIRNLPFDVTKEEVKQRFTVFGEVESLSLVL 594

Query:   460 HQVTKRPKGTGFLKFXXXXXXXXXXXXXXXXXGLGIFLKGRQLTVXXXXXXXXXXXXEID 519
             H+VTKRP+GT F+KF                 G+G+ LKGRQL V            E+ 
Sbjct:   595 HKVTKRPEGTAFVKFKTADASVAAISAADTASGVGVLLKGRQLNVMRAVGKKAAKDIELK 654

Query:   520 KSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTR 579
             K++ +  DHRNLYLAKEG IL+ TPAAEGVS +DM KR+ LHE KM  LQSPNFHVSRTR
Sbjct:   655 KTEEKNVDHRNLYLAKEGQILDDTPAAEGVSAEDMDKRRRLHENKMKMLQSPNFHVSRTR 714

Query:   580 LVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFV 639
             LVIYNLPKSM  K L +L +DAV SRA+KQKP I+QIKFLQ+ KKGKVDTK+YSRGVAFV
Sbjct:   715 LVIYNLPKSMNPKQLNRLLVDAVTSRATKQKPCIRQIKFLQNEKKGKVDTKNYSRGVAFV 774

Query:   640 EFTEHQHALVALRVLNNNPSKLFYHH 665
             EFTEH+HALVALRVLNNNP      H
Sbjct:   775 EFTEHEHALVALRVLNNNPETFGPQH 800

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

UNIPROTKB|Q9NW13 RBM28 "RNA-binding protein 28" [Homo sapiens (taxid:9606)]

 Score = 503 (182.1 bits), Expect = 8.5e-48, P = 8.5e-48
 Identities = 144/459 (31%), Positives = 207/459 (45%)

Query:   215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
             +K +LIIRN+ FK   +++K +F+  G V  V IP   D G  +GF FV+F    +A  A
Sbjct:   112 KKARLIIRNLSFKCSEDDLKTVFAQFGAVLEVNIPRKPD-GKMRGFGFVQFKNLLEAGKA 170

Query:   275 IQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGV-QNKXXXXXXXXXXXXXXXXXXXXXX 333
             ++  N ++   R +AVDWAV K+ Y    + + + + K                      
Sbjct:   171 LKGMNMKEIKGRTVAVDWAVAKDKYKDTQSVSAIGEEKSHESKHQESVKKKGREEEDMEE 230

Query:   334 XXXXXXXKEDLPSNADFDEEVDIARKVLNKXXXXXXXXXXXXXXXALVKGNKEQDSDKTV 393
                     +D   +  FD+E +    + +K               A  K +   + D  +
Sbjct:   231 EENDDDDDDDDEEDGVFDDEDEEEENIESKVTKPVQIQKRAVKRPAPAKSSDHSEEDSDL 290

Query:   394 NESAKVSD----VXXXXXXXXXXXXXXQTEGEDELQ--------NTIFICNLPFDLDNEE 441
              ES  + D                   Q   + + +         T+FI NL FD + EE
Sbjct:   291 EESDSIDDGEELAQSDTSTEEQEDKAVQVSNKKKRKLPSDVNEGKTVFIRNLSFDSEEEE 350

Query:   442 VKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFXXXXXXXXXXXXXXXXXGLG-IFLKGR 500
             + +    FGE+     VLH  T+  KG  F +F                   G + L GR
Sbjct:   351 LGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLAASPENEAGGLKLDGR 410

Query:   501 QLTVXXXXXXXXXXXXEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQML 560
             QL V            +  K K  T   RNLYLA+EGLI  GT AAEGVS  DM+KR+  
Sbjct:   411 QLKVDLAVTRDEAAKLQTTKVKKPTGT-RNLYLAREGLIRAGTKAAEGVSAADMAKRERF 469

Query:   561 HEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPV-IKQIKFL 619
                K  KL+  N  VSRTRL ++NLPK++ +K L+KL + A     S +K V IK+ + +
Sbjct:   470 ELLKHQKLKDQNIFVSRTRLCLHNLPKAVDDKQLRKLLLSAT----SGEKGVRIKECRVM 525

Query:   620 QSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
             + LK    + K  S G AF EF EH+HAL ALR++NNNP
Sbjct:   526 RDLKGVHGNMKGQSLGYAFAEFQEHEHALKALRLINNNP 564

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

UNIPROTKB|E1BLD4 RBM28 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 377 (137.8 bits), Expect = 1.2e-45, Sum P(2) = 1.2e-45
 Identities = 94/233 (40%), Positives = 124/233 (53%)

Query:   427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFXXXXXXXXXXXX 486
             T+FI NL FD + E++ +    FG++     VLH  T+  KG  F +F            
Sbjct:   333 TVFIRNLSFDSEEEDLGELLQQFGDLKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLEA 392

Query:   487 XX-XXXGLGIFLKGRQLTVXXXXXXXXXXXXEIDKSKNETNDHRNLYLAKEGLILEGTPA 545
                   G G+ L GRQL V               K K  T   RNLYLA+EGLI  GT A
Sbjct:   393 ASPEAEGGGLKLDGRQLKVDLAVTRDEAAKLRTKKVKKPTGT-RNLYLAREGLIRAGTKA 451

Query:   546 AEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSR 605
             AEGVS  DM+KR+     K  KL+  N  VSRTRL ++NLPK++ +K L+KL +++  +R
Sbjct:   452 AEGVSAADMAKRERFELLKHQKLKDQNIFVSRTRLCLHNLPKAVDDKQLRKLLLNS--TR 509

Query:   606 ASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
               K    IK+ + ++ LK      K  S G AF EF EH+HAL ALR +NNNP
Sbjct:   510 GEKAVR-IKECRVMRDLKGAYGKIKGQSLGYAFAEFQEHEHALAALRHINNNP 561

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2RIB8 RBM28 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 378 (138.1 bits), Expect = 6.1e-45, Sum P(2) = 6.1e-45
 Identities = 97/235 (41%), Positives = 127/235 (54%)

Query:   427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFXXXXXXXXXXXX 486
             T+FI NL FD + EE+ +    FG++     VLH  T+  KG  F +F            
Sbjct:   328 TVFIRNLSFDSEEEELGELLQQFGDLKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLEA 387

Query:   487 XX-XXXGLGIFLKGRQLTVXXXXXXXXXXXXEIDKSKNETNDHRNLYLAKEGLILEGTPA 545
                   G G+ L GRQL V            +  K K  T   RNLYLA+EGLI  GT A
Sbjct:   388 ASPETEGGGLKLDGRQLRVDLAVTRDEAAKLQTKKVKKPTGT-RNLYLAREGLIRAGTKA 446

Query:   546 AEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSR 605
             AEGVS  DM+KR+     K  KL+  N  VS+TRL ++NLPK + +K L+KL ++A  +R
Sbjct:   447 AEGVSAADMAKRERFELLKHQKLKDQNIFVSQTRLCLHNLPKGVDDKELRKLLLNA--TR 504

Query:   606 ASKQKPVIKQIKFLQSLK--KGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
               K    +K+ + ++ LK   GKV  K  S G AF EF EH+HAL ALR +NNNP
Sbjct:   505 GEKGVR-LKECRVMRDLKGVHGKV--KGQSLGYAFAEFQEHEHALTALRHINNNP 556

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-040426-960 rbm28 "RNA binding motif protein 28" [Danio rerio (taxid:7955)]

 Score = 340 (124.7 bits), Expect = 1.6e-43, Sum P(2) = 1.6e-43
 Identities = 88/234 (37%), Positives = 121/234 (51%)

Query:   427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPV-LHQVTKRPKGTGFLKFXXXXXXXXXXX 485
             TIFI NL FD + E +++    FGE+ S+V V ++  T   KG  F +F           
Sbjct:   440 TIFIRNLSFDSEEEGLEEVLLQFGEL-SYVRVVMNPDTGVSKGCAFAQFKSKEAAEKCIA 498

Query:   486 XXXXXXGL-GIFLKGRQLTVXXXXXXXXXXXXEIDKSKNETNDHRNLYLAKEGLILEGTP 544
                      GI L GR+L +            +  K K  T   RNLYLA+EGLI  GT 
Sbjct:   499 AALDEKEFSGIKLDGRRLNILMAINRDDAAKFKDKKVKTHTGS-RNLYLAREGLIRAGTK 557

Query:   545 AAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVS 604
             AAEG+S+ D++KR    E K  +L+  N +VS+TRL ++NLPKS+ +  L  LC+ A   
Sbjct:   558 AAEGISEADIAKRTRFEELKRARLKDINVYVSKTRLCVHNLPKSVDKNKLFNLCVSAAGG 617

Query:   605 RASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
             +  +    I + + +   K  K      S G  FVEF EH+HA+ ALR LNNNP
Sbjct:   618 KGVR----IIECRIMYDKKPVKGQVMGQSLGYGFVEFQEHEHAIQALRHLNNNP 667

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

RGD|1311336 Rbm28 "RNA binding motif protein 28" [Rattus norvegicus (taxid:10116)]

 Score = 369 (135.0 bits), Expect = 5.4e-43, Sum P(2) = 5.4e-43
 Identities = 95/234 (40%), Positives = 124/234 (52%)

Query:   427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFXXXXXXXXXXXX 486
             T+FI NL FD + E + +    FG++     VLH  T+  KG  F +F            
Sbjct:   326 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRIVLHPDTEHSKGCAFAQFVTQEAAQKCLAA 385

Query:   487 XX-XXXGLGIFLKGRQLTVXXXXXXXXXXXXEIDKSKNETNDHRNLYLAKEGLILEGTPA 545
                   G G+ L GRQL V            +  K K  T   RNLYLA+EGLI  GT A
Sbjct:   386 ASPETEGGGLKLDGRQLKVDLAVTRDEAAKLQTKKVKKPTGT-RNLYLAREGLIRAGTKA 444

Query:   546 AEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSR 605
             AEGVS  DM+KR+     K  KL++ N  VS+TRL ++NLPKS+ +K L+KL + A    
Sbjct:   445 AEGVSAADMAKRERFELLKHQKLKNQNIFVSQTRLCLHNLPKSVDDKQLRKLLLQAT--- 501

Query:   606 ASKQKPV-IKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
                +K V IK+ + ++ LK      K  S G AFVEF +H+HAL ALR  NNNP
Sbjct:   502 -GGEKGVRIKECRVMRDLKAVHGKMKGQSLGYAFVEFQKHEHALRALRHFNNNP 554

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

GO:0005794 "Golgi apparatus" evidence=ISO

MGI|MGI:2655711 Rbm28 "RNA binding motif protein 28" [Mus musculus (taxid:10090)]

 Score = 367 (134.2 bits), Expect = 6.0e-43, Sum P(2) = 6.0e-43
 Identities = 93/233 (39%), Positives = 124/233 (53%)

Query:   427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFXXXXXXXX-XXX 485
             T+FI NL FD + E + +    FG++     VLH  T+  KG  F +F            
Sbjct:   326 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 385

Query:   486 XXXXXXGLGIFLKGRQLTVXXXXXXXXXXXXEIDKSKNETNDHRNLYLAKEGLILEGTPA 545
                   G G+ L GRQL V            +  K K  T   RNLYLA+EGLI  GT A
Sbjct:   386 ASLEAEGGGLKLDGRQLKVDLAVTRDEAAKLQTKKVKKPTGT-RNLYLAREGLIRAGTKA 444

Query:   546 AEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSR 605
             AEGVS  DM+KR+     K  KL++ N  VS+TRL ++NLPK++ +K L+KL ++A  +R
Sbjct:   445 AEGVSAADMAKRERFELLKHQKLKNQNIFVSQTRLCLHNLPKAVDDKQLRKLLLEA--TR 502

Query:   606 ASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
               K    IK+ + ++ LK      K  S G AF EF +H+HAL ALR  NNNP
Sbjct:   503 GEKGVR-IKECRVMRDLKGVHGKMKGQSLGYAFAEFQKHEHALRALRHFNNNP 554

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008380 "RNA splicing" evidence=IEA

UNIPROTKB|G3MZL2 RBM28 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 377 (137.8 bits), Expect = 3.0e-34, Sum P(2) = 3.0e-34
 Identities = 94/233 (40%), Positives = 124/233 (53%)

Query:   427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFXXXXXXXXXXXX 486
             T+FI NL FD + E++ +    FG++     VLH  T+  KG  F +F            
Sbjct:   187 TVFIRNLSFDSEEEDLGELLQQFGDLKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLEA 246

Query:   487 XX-XXXGLGIFLKGRQLTVXXXXXXXXXXXXEIDKSKNETNDHRNLYLAKEGLILEGTPA 545
                   G G+ L GRQL V               K K  T   RNLYLA+EGLI  GT A
Sbjct:   247 ASPEAEGGGLKLDGRQLKVDLAVTRDEAAKLRTKKVKKPTGT-RNLYLAREGLIRAGTKA 305

Query:   546 AEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSR 605
             AEGVS  DM+KR+     K  KL+  N  VSRTRL ++NLPK++ +K L+KL +++  +R
Sbjct:   306 AEGVSAADMAKRERFELLKHQKLKDQNIFVSRTRLCLHNLPKAVDDKQLRKLLLNS--TR 363

Query:   606 ASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
               K    IK+ + ++ LK      K  S G AF EF EH+HAL ALR +NNNP
Sbjct:   364 GEKAVR-IKECRVMRDLKGAYGKIKGQSLGYAFAEFQEHEHALAALRHINNNP 415

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

WB|WBGene00011043 rbm-28 [Caenorhabditis elegans (taxid:6239)]

 Score = 269 (99.8 bits), Expect = 1.7e-33, Sum P(2) = 1.7e-33
 Identities = 71/238 (29%), Positives = 108/238 (45%)

Query:   428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFXXXXXXXXXXXXX 487
             +F+ NL +D   E +K+  S FG++   +   ++ +   KGT F+ F             
Sbjct:   265 VFLRNLSYDTKEELIKEELSKFGKIDLAIICKYKDSGHSKGTAFVHFSTPIEASNCIEGV 324

Query:   488 XXXXGLGIFLKGRQLTVXXXXXXXXXXXXEIDKSKNETNDHRNLYLAKEGLILEGTPAAE 547
                   G+ +  R +              E +K      D RNL LA+ GLI +GT AA 
Sbjct:   325 ED----GVIIDNRLVKANLAIPRKEAADMEKEKLTKVPKDKRNLRLARFGLIRDGTAAAA 380

Query:   548 GVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRAS 607
             G+S DD +KR+ + E    KL++ N  +S  RL I+NLP+ + +  LK+L       + +
Sbjct:   381 GMSKDDAAKRERIAEAMRKKLENTNMFISPVRLCIHNLPQKINDVKLKELA-----QKFT 435

Query:   608 KQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHH 665
                 +I + +     K+   D K  S G  FV F EH HAL  L+ LNNN       H
Sbjct:   436 SPGALITECRVWMDKKRLTPDGKPKSSGFGFVAFKEHMHALECLKKLNNNAETFHKDH 493

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0009058 "biosynthetic process" evidence=IEA

GO:0030170 "pyridoxal phosphate binding" evidence=IEA

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0040026 "positive regulation of vulval development" evidence=IMP

ASPGD|ASPL0000078272 AN4330 [Emericella nidulans (taxid:162425)]

 Score = 137 (53.3 bits), Expect = 4.0e-31, Sum P(5) = 4.0e-31
 Identities = 35/98 (35%), Positives = 55/98 (56%)

Query:   205 RQLGGEGSKTQKWKLIIRNIPFKAKVNE-IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFV 263
             +Q   + + TQ  KLI+RN+P+  K  E +   F   G V  V +P    + L+ GF FV
Sbjct:   138 KQREQQKADTQPPKLIVRNLPWSIKTPEDLAAHFRSFGKVKYVTLPKK-GSQLA-GFGFV 195

Query:   264 KFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSS 301
                 K++AE A++  NG++   R +AVDWAV K ++ +
Sbjct:   196 VLRGKKNAEKALEAVNGKEVDGRTLAVDWAVEKEVWEN 233

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

---

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	Length	Definition	E-value
Query	676
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	4e-34
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-27
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-23
smart00360	73	smart00360, RRM, RNA recognition motif	6e-20
smart00360	73	smart00360, RRM, RNA recognition motif	8e-16
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-15
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-15
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	9e-15
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	9e-15
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-14
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	5e-14
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	6e-14
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-13
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-13
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-13
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-12
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-12
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-12
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	3e-12
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	6e-12
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	8e-12
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	9e-12
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-11
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-11
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	6e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-10
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	2e-10
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-10
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-10
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-10
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	5e-10
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	6e-10
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	8e-10
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	9e-10
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	1e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-09
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-09
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-09
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-09
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	3e-09
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	3e-09
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-09
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	3e-09
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-09
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-09
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-09
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	5e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	8e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	9e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-08
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-08
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-08
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-08
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-08
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-08
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-08
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	4e-08
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	4e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-08
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	5e-08
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	5e-08
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	5e-08
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	5e-08
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	8e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	8e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	9e-08
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	9e-08
smart00360	73	smart00360, RRM, RNA recognition motif	1e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-07
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-07
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-07
cd12677	156	cd12677, RRM4_Nop4p, RNA recognition motif 4 in ye	1e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-07
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-07
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-07
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-07
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	3e-07
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	3e-07
cd12277	86	cd12277, RRM3_MEI2_EAR1_like, RNA recognition moti	4e-07
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	4e-07
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	4e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	5e-07
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-07
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	5e-07
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	5e-07
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	6e-07
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	7e-07
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	9e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	9e-07
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	9e-07
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	9e-07
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	9e-07
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	9e-07
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	9e-07
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	9e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-06
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	1e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-06
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	1e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-06
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	1e-06
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	1e-06
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	2e-06
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-06
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-06
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-06
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	2e-06
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-06
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-06
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	3e-06
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-06
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-06
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-06
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-06
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-06
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-06
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	4e-06
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	4e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-06
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	4e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	4e-06
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	4e-06
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	4e-06
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	4e-06
smart00360	73	smart00360, RRM, RNA recognition motif	5e-06
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	5e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	5e-06
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	5e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-06
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	5e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-06
cd12515	75	cd12515, RRM5_RBM12_like, RNA recognition motif 5	6e-06
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	6e-06
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	6e-06
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	7e-06
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	7e-06
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	8e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	8e-06
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	9e-06
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-06
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-05
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-05
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	1e-05
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	1e-05
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-05
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	1e-05
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-05
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	1e-05
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-05
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	2e-05
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-05
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	2e-05
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	2e-05
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	2e-05
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-05
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	3e-05
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-05
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	3e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	3e-05
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	3e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	3e-05
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	3e-05
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	4e-05
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	5e-05
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	5e-05
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	5e-05
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	6e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	6e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	6e-05
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	6e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	7e-05
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	7e-05
cd12502	72	cd12502, RRM2_RMB19, RNA recognition motif 2 in RN	8e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	8e-05
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	8e-05
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	8e-05
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	9e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	9e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	9e-05
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	9e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-04
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-04
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	1e-04
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	1e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-04
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-04
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	1e-04
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	1e-04
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	1e-04
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	1e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-04
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-04
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	2e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-04
cd12750	77	cd12750, RRM5_RBM12B, RNA recognition motif 5 in R	2e-04
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	2e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	2e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-04
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	2e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-04
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	2e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	2e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	3e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	3e-04
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	3e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	3e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-04
cd12331	79	cd12331, RRM_NRD1_SEB1_like, RNA recognition motif	3e-04
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	3e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-04
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	3e-04
cd12504	77	cd12504, RRM2_hnRNPH_like, RNA recognition motif 2	3e-04
cd12569	72	cd12569, RRM4_RBM19, RNA recognition motif 4 in RN	3e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	4e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	4e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	4e-04
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	4e-04
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	4e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	4e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	4e-04
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	4e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	5e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	5e-04
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	5e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	5e-04
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	6e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	6e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	6e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	6e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	6e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	6e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	6e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	6e-04
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	6e-04
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	7e-04
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	7e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	8e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	8e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	8e-04
cd12492	85	cd12492, RRM2_RBM46, RNA recognition motif 2 found	8e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	8e-04
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	9e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	9e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	9e-04
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	0.001
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	0.001
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	0.001
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.001
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.001
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	0.001
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	0.001
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	0.001
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	0.001
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	0.001
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	0.001
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	0.001
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.001
cd12506	75	cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition m	0.001
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	0.001
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	0.001
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	0.001
cd12514	73	cd12514, RRM4_RBM12_like, RNA recognition motif 4	0.001
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	0.002
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	0.002
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.002
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.002
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	0.002
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.002
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	0.002
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.002
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.002
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.002
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.002
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	0.002
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	0.002
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.002
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	0.002
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	0.002
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	0.002
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	0.002
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	0.002
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.002
cd12490	85	cd12490, RRM2_ACF, RNA recognition motif 2 in vert	0.002
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	0.002
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.003
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.003
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	0.003
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	0.003
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	0.003
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	0.003
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.003
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	0.004
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	0.004
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.004
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	0.004
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.004
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.004
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	0.004
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	0.004
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	0.004
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.004
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	0.004
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	0.004
cd12746	78	cd12746, RRM2_RBM12B, RNA recognition motif 2 in R	0.004

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score =  125 bits (315), Expect = 4e-34
 Identities = 47/81 (58%), Positives = 58/81 (71%)

Query: 578 TRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVA 637
           TRL I NLPKS+ EK LK+L + AV  RA K+KP IKQ+K ++ LK+   + K  S+G  
Sbjct: 1   TRLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYG 60

Query: 638 FVEFTEHQHALVALRVLNNNP 658
           FVEFT H+HAL ALR LNNNP
Sbjct: 61  FVEFTNHEHALKALRALNNNP 81

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score =  105 bits (264), Expect = 2e-27
 Identities = 44/77 (57%), Positives = 54/77 (70%), Gaps = 1/77 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +LI+RN+PFK    ++K +FSP G VW V IP   D G  KGFAFV+FT K DAE AI+ 
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPD-GKKKGFAFVQFTSKADAEKAIKG 59

Query: 278 FNGQKFGKRPIAVDWAV 294
            NG+K   RP+AVDWAV
Sbjct: 60  VNGKKIKGRPVAVDWAV 76

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 94.2 bits (235), Expect = 2e-23
 Identities = 37/81 (45%), Positives = 48/81 (59%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T+FI NLPFD   EE+K+ FS FGEV     V  ++T   KGT F+KFKT E+A   + A
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

Query: 487 SKTTSGLGIFLKGRQLTVLKA 507
           +      G+ L GR+L V  A
Sbjct: 62  ADNAEDSGLSLDGRRLIVTLA 82

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 83.8 bits (208), Expect = 6e-20
 Identities = 28/73 (38%), Positives = 45/73 (61%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L + N+P      E++++FS  G V +V +  + +TG SKGFAFV+F  + DAE A++ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 278 FNGQKFGKRPIAV 290
            NG++   RP+ V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 72.2 bits (178), Expect = 8e-16
 Identities = 30/78 (38%), Positives = 43/78 (55%), Gaps = 5/78 (6%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T+F+ NLP D   EE+++ FS FG+V S   V  + T + KG  F++F++ E A  A+ A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 487 SKTTSGLGIFLKGRQLTV 504
                  G  L GR L V
Sbjct: 61  LN-----GKELDGRPLKV 73

Length = 73

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 71.5 bits (176), Expect = 1e-15
 Identities = 27/71 (38%), Positives = 41/71 (57%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           NIP+ A   ++ ++FS VG V +  +  + DTG  KG+ F +F     A SAI+  NG +
Sbjct: 5   NIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYE 64

Query: 283 FGKRPIAVDWA 293
           F  R + VD+A
Sbjct: 65  FNGRALRVDFA 75

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 71.6 bits (176), Expect = 1e-15
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+P      +++++FS  G + +V I  +   G SKGFAFV+F    DAE A++  
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 279 NGQKFGKRPIAVD 291
           NG++   R + V 
Sbjct: 60  NGKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 71.1 bits (175), Expect = 2e-15
 Identities = 27/48 (56%), Positives = 32/48 (66%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
          V  KGS + RGFGYV FA+ EDA RA+E K  T  GGRKI V+ A  +
Sbjct: 32 VKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVEFAKKK 79

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 69.2 bits (170), Expect = 9e-15
 Identities = 27/70 (38%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+P      ++KD+FS  G + ++ I  + +TG SKGFAFV+F  + DAE A++  
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 279 NGQKFGKRPI 288
           NG++ G R +
Sbjct: 60  NGKELGGREL 69

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 69.1 bits (170), Expect = 9e-15
 Identities = 27/73 (36%), Positives = 46/73 (63%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           + N+   A  ++++++F P G +  VY+  + +TG S+GFAFV F  + DAE AI+K NG
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

Query: 281 QKFGKRPIAVDWA 293
             +    ++V+WA
Sbjct: 64  FGYDNLILSVEWA 76

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 68.4 bits (168), Expect = 2e-14
 Identities = 29/76 (38%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KLI+RN+PF+A   E++++FSP G V +V +P   D G  +GFAFV+F  K++A++A++ 
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFD-GSHRGFAFVEFVTKQEAQNAMEA 60

Query: 278 FNGQKFGKRPIAVDWA 293
                   R + +++A
Sbjct: 61  LKSTHLYGRHLVLEYA 76

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 68.4 bits (168), Expect = 2e-14
 Identities = 27/78 (34%), Positives = 44/78 (56%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L + N+P+     ++KD+F   G V +  +  + +TG S+GF FV+     +A +AI+K
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 278 FNGQKFGKRPIAVDWAVP 295
            NG  FG R + V+ A P
Sbjct: 61  LNGTDFGGRTLTVNEARP 78

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 67.6 bits (165), Expect = 5e-14
 Identities = 35/83 (42%), Positives = 47/83 (56%), Gaps = 2/83 (2%)

Query: 218 KLIIRNIPFKAKVNE-IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           KLIIRN+P+  K    +K +F   G V    IP      L  GFAFV    +++AE A++
Sbjct: 2   KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLC-GFAFVTMKKRKNAEIALE 60

Query: 277 KFNGQKFGKRPIAVDWAVPKNIY 299
             NG +   RP+AVDWAV KN +
Sbjct: 61  NTNGLEIDGRPVAVDWAVQKNRW 83

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 66.8 bits (164), Expect = 6e-14
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +RN+P      ++++ FSP G V  V +  N D    +GFAFV+F    DAE+A++K 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 279 NGQKFGKRPI 288
           NG     R +
Sbjct: 59  NGLVLDGRTL 68

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 66.1 bits (162), Expect = 1e-13
 Identities = 23/78 (29%), Positives = 44/78 (56%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +RN+P+     ++++ FS VG +   ++  +  +   +GF +V F  + DA+ A+++ 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 279 NGQKFGKRPIAVDWAVPK 296
              KFG R I V++A  K
Sbjct: 62  KKTKFGGRKIHVEFAKKK 79

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 65.4 bits (160), Expect = 2e-13
 Identities = 26/73 (35%), Positives = 44/73 (60%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+ ++   ++++ +F   G V +VYIP +  T  S+GFAFV+F  KRDAE A+   
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 279 NGQKFGKRPIAVD 291
           +G++   R + V 
Sbjct: 61  DGKELDGRELRVQ 73

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 64.2 bits (157), Expect = 4e-13
 Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 6/77 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +F+ NLP D   E++++ FS FGE+ S   ++     + KG  F++F++ E A  A+ A 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVR-IVRDKDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 488 KTTSGLGIFLKGRQLTV 504
                 G  L GR+L V
Sbjct: 60  N-----GKELDGRKLKV 71

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 69.2 bits (168), Expect = 1e-12
 Identities = 34/133 (25%), Positives = 64/133 (48%)

Query: 210 EGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKR 269
           + SK +   L + N+P+     +++++F   G V  V +  + +TG S+GFAFV+F  + 
Sbjct: 109 QKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEE 168

Query: 270 DAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDA 329
            AE AI++ NG++   RP+ V  A P +   S  +     +     S   +      D+ 
Sbjct: 169 SAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNL 228

Query: 330 ETASDDSNSSEKE 342
              +    ++E+E
Sbjct: 229 YVGNLPLKTAEEE 241

Length = 306

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 62.6 bits (153), Expect = 2e-12
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +F+ NLP D   E++K  FS FG + S   ++   T R KG  F++F+  E A  A+ A 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIR-IVRDETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 488 KTTSGLGIFLKGRQLT 503
                 G  L GR+L 
Sbjct: 60  N-----GKELGGRELR 70

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 62.8 bits (153), Expect = 2e-12
 Identities = 24/75 (32%), Positives = 43/75 (57%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +RN+    + ++++ +F   G + +VYIP +  T   +GFA+V+F   RDAE A+   
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 279 NGQKFGKRPIAVDWA 293
           +  +F  R I + +A
Sbjct: 63  DRTRFLGREIEIQFA 77

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 62.6 bits (153), Expect = 3e-12
 Identities = 22/77 (28%), Positives = 48/77 (62%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           W + +  +  +A+  ++ D F+  G + N+++  +  TG  KG+A +++  K++A++AI+
Sbjct: 7   WIIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIE 66

Query: 277 KFNGQKFGKRPIAVDWA 293
             NG++   + I+VDWA
Sbjct: 67  GLNGKELLGQTISVDWA 83

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 61.3 bits (149), Expect = 6e-12
 Identities = 30/79 (37%), Positives = 50/79 (63%), Gaps = 4/79 (5%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHN-TDTGLSKGFAFVKFTCKRDAESAIQ 276
           K+++RNIPF+A V E++++FS  G +  V +P   T TG  +GF FV F  K+DA+ A +
Sbjct: 2   KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61

Query: 277 --KFNGQKFGKRPIAVDWA 293
               +   +G+R + ++WA
Sbjct: 62  ALCHSTHLYGRR-LVLEWA 79

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 61.1 bits (149), Expect = 8e-12
 Identities = 28/81 (34%), Positives = 44/81 (54%), Gaps = 5/81 (6%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            +++ NLP+++  E++K  F  FGEV S   +  + T R +G GF++ +T E A AA+  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 487 SKTTSGLGIFLKGRQLTVLKA 507
              T        GR LTV +A
Sbjct: 61  LNGTD-----FGGRTLTVNEA 76

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 60.8 bits (148), Expect = 9e-12
 Identities = 30/78 (38%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +F+ NLPF    EE+++ F AFGE+      L + TKR KG  F+ F   E A  A S  
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 488 KTTSGLGIFLKGRQLTVL 505
                 G   +GR L VL
Sbjct: 62  D-----GSIFQGRLLHVL 74

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 60.2 bits (146), Expect = 2e-11
 Identities = 23/78 (29%), Positives = 40/78 (51%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +RN+ F     ++ D FS V  + +  +  + +TG S+G+ FV F    DA+ A+ K 
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 279 NGQKFGKRPIAVDWAVPK 296
             +K   R + +D A  +
Sbjct: 62  KNKKLHGRILRLDIAERR 79

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 59.9 bits (146), Expect = 2e-11
 Identities = 23/65 (35%), Positives = 38/65 (58%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL +  +P  A   +++ +F   G +  V I  + DTG SKG AFVKF+ + +A+ AI+ 
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 278 FNGQK 282
            +G+ 
Sbjct: 61  LHGKV 65

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 58.4 bits (142), Expect = 6e-11
 Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 5/77 (6%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +F+ N+P+D   E++ + FS  G VVSF  V  + T +PKG GF +F+ +E A +A+   
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAI--- 57

Query: 488 KTTSGLGIFLKGRQLTV 504
           +  +  G    GR L V
Sbjct: 58  RNLN--GYEFNGRALRV 72

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 26/76 (34%), Positives = 42/76 (55%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL +  +  +    E++ +FS  G V  V +  + +TG S+GF FV F    DA++AI+ 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 278 FNGQKFGKRPIAVDWA 293
            NG++   R I V+ A
Sbjct: 63  LNGKELEGRVIKVEKA 78

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 26/72 (36%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           + +RN+PF     ++KD+F   G V    +  + D G SKGF  V F    DA+ AI+ F
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59

Query: 279 NGQKFGKRPIAV 290
           NG     R + V
Sbjct: 60  NGYDLEGRELEV 71

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 4/76 (5%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSK---GFAFVKFTCKRDAESA 274
           ++ +RN+ FK   ++++ +FS  G V ++ IP   D    +   GFAFV F     AE+A
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 275 IQKFNGQKFGKRPIAV 290
           +Q  NG + G R I+V
Sbjct: 62  LQL-NGTELGGRKISV 76

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 56.6 bits (137), Expect = 3e-10
 Identities = 24/73 (32%), Positives = 44/73 (60%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L +RN+P+  K ++++ +FS  G +  V++  +  +G SKGFA+V F    DA  A ++
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 278 FNGQKFGKRPIAV 290
            +G+ F  R I +
Sbjct: 64  LDGKVFQGRLIHI 76

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 56.2 bits (136), Expect = 4e-10
 Identities = 25/60 (41%), Positives = 35/60 (58%)

Query: 233 IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW 292
           ++  F+P G + +  +  +  TG SKG+ FV F  K DAE+AIQ  NGQ  G R I  +W
Sbjct: 16  LRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAIRTNW 75

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 55.7 bits (135), Expect = 5e-10
 Identities = 24/75 (32%), Positives = 43/75 (57%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+P +    + +++ SP G V   ++ ++  TG SKG+ FV++  K  A  A  + 
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 279 NGQKFGKRPIAVDWA 293
           +G++ G R + VDWA
Sbjct: 62  DGKQIGGRKLQVDWA 76

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 55.6 bits (135), Expect = 6e-10
 Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLV-WNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN 279
           +R +PF A   +I+D FS + +    ++I    D G   G A+V+F    DA  A++K +
Sbjct: 4   LRGLPFSATEEDIRDFFSGLDIPPDGIHI-VYDDDGRPTGEAYVEFASPEDARRALRK-H 61

Query: 280 GQKFGKRPIAV 290
             K G R I V
Sbjct: 62  NNKMGGRYIEV 72

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 55.3 bits (134), Expect = 8e-10
 Identities = 19/57 (33%), Positives = 33/57 (57%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAA 483
            IF+  LP+   ++ +++ FS FGE+   V +  + T + +G GF+ FK  E+A  A
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA 58

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 55.0 bits (133), Expect = 9e-10
 Identities = 24/69 (34%), Positives = 38/69 (55%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L +RN+PF     E++++F   G +  V++P + +T  SKGFAFV F     A  A  +
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 278 FNGQKFGKR 286
            +G  F  R
Sbjct: 61  LDGSIFQGR 69

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 26/74 (35%), Positives = 38/74 (51%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           W + + N+P  A  + +  +FSP G V NV +  +  T   KG+ FV  T   +A SAI 
Sbjct: 2   WCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIA 61

Query: 277 KFNGQKFGKRPIAV 290
             NG + G R + V
Sbjct: 62  SLNGYRLGGRVLQV 75

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 23/72 (31%), Positives = 42/72 (58%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+ F    ++++ +F P G +  V +  + +TG SKG+ F++F    DA+ A+++ 
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 279 NGQKFGKRPIAV 290
           NG +   RPI V
Sbjct: 61  NGFELAGRPIKV 72

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 54.1 bits (130), Expect = 2e-09
 Identities = 21/76 (27%), Positives = 45/76 (59%), Gaps = 1/76 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K++++N+PF+A   +++ +FS  G + +V +P   D   ++GFAFV+F+  ++A +A+  
Sbjct: 2   KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQS-ARGFAFVEFSTAKEALNAMNA 60

Query: 278 FNGQKFGKRPIAVDWA 293
                   R + + +A
Sbjct: 61  LKDTHLLGRRLVLQYA 76

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +  +P      E++ +FSP G +    I  +  TGLS+G  F++F  + +AE AI+  
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 279 NGQKF--GKRPIAVDWA 293
           NG        PI V +A
Sbjct: 63  NGTIPPGATEPITVKFA 79

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 53.9 bits (129), Expect = 2e-09
 Identities = 27/63 (42%), Positives = 38/63 (60%)

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
           ++IK  F+P G + +  +  +  TG SKG+ FV F  K DAE+AIQ+  GQ  G R I  
Sbjct: 16  DDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT 75

Query: 291 DWA 293
           +WA
Sbjct: 76  NWA 78

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 53.9 bits (130), Expect = 3e-09
 Identities = 28/77 (36%), Positives = 38/77 (49%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           LII  +P      E + +F  VG V N  I  +  TG S GF FV +    DA+ AI+  
Sbjct: 3   LIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTL 62

Query: 279 NGQKFGKRPIAVDWAVP 295
           NG +   + I V +A P
Sbjct: 63  NGLQLQNKRIKVAYARP 79

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 54.6 bits (131), Expect = 3e-09
 Identities = 27/70 (38%), Positives = 38/70 (54%), Gaps = 3/70 (4%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T+F+ NLP+D   E +   FS FG V   +PV+ + T R KGTGF+ FK      A +  
Sbjct: 3   TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKN 62

Query: 487 SK---TTSGL 493
           +    +TS L
Sbjct: 63  APAAGSTSLL 72

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 25/67 (37%), Positives = 38/67 (56%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +F+ NL FD D + + + F  +GE+ S        + RPKG G+++F + EAA AA+ A 
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 488 KTTSGLG 494
             T  LG
Sbjct: 61  GGTDLLG 67

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 53.9 bits (129), Expect = 3e-09
 Identities = 30/81 (37%), Positives = 43/81 (53%), Gaps = 2/81 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L I  +P      +++DMFS  G + N  +  +  TGLS+G AF++F  + +AE AI  F
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 279 NGQK--FGKRPIAVDWAVPKN 297
           NG K      PI V +A   N
Sbjct: 63  NGHKPPGSSEPITVKFAANPN 83

This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 53.3 bits (128), Expect = 4e-09
 Identities = 30/77 (38%), Positives = 45/77 (58%), Gaps = 5/77 (6%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +F+ N+P++   E++K  FS  G VVSF  V  + T +PKG GF ++K  E    A+SA 
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQE---TALSAM 57

Query: 488 KTTSGLGIFLKGRQLTV 504
           +  +G  +   GRQL V
Sbjct: 58  RNLNGYEL--NGRQLRV 72

This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. . Length = 75

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 53.3 bits (128), Expect = 4e-09
 Identities = 25/71 (35%), Positives = 43/71 (60%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           NIP++A   ++KD+FS VG V +  + ++ +TG  KG+ F ++  +  A SA++  NG +
Sbjct: 5   NIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYE 64

Query: 283 FGKRPIAVDWA 293
              R + VD A
Sbjct: 65  LNGRQLRVDNA 75

This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. . Length = 75

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 53.0 bits (128), Expect = 5e-09
 Identities = 25/82 (30%), Positives = 39/82 (47%), Gaps = 5/82 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           N +F+  L      +E++  FS FG V   + +    T   +G GF+ F++VE A AA+ 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 486 ASKTTSGLGIFLKGRQLTVLKA 507
                      L+GR + V KA
Sbjct: 62  DLNGKE-----LEGRVIKVEKA 78

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 52.9 bits (128), Expect = 5e-09
 Identities = 23/70 (32%), Positives = 37/70 (52%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           N+ F     +I ++FS  G +  + +  +  T    GF FV++  + DAE+A++  NG K
Sbjct: 5   NLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNGTK 64

Query: 283 FGKRPIAVDW 292
              R I VDW
Sbjct: 65  LDDRIIRVDW 74

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 51.7 bits (125), Expect = 8e-09
 Identities = 23/61 (37%), Positives = 34/61 (55%), Gaps = 5/61 (8%)

Query: 233 IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW 292
           +  +FSP G V  + +          GFAFV+F+ +  AE A+Q  NG  FG RP+ VD+
Sbjct: 1   LYKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 293 A 293
           +
Sbjct: 56  S 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 56.9 bits (136), Expect = 9e-09
 Identities = 43/218 (19%), Positives = 81/218 (37%), Gaps = 10/218 (4%)

Query: 310 NKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDE-EVDIARKVLNKLTSTT 368
           +K      S  +    +D       +    E+      A+  E  +++  + +    S  
Sbjct: 3   SKNLKGPHSSFESVKPEDIESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEISPP 62

Query: 369 GSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTI 428
                LS +       + ++ +       K  +     SS+S     K  E      NT+
Sbjct: 63  SKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKE----ENNTL 118

Query: 429 FICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASK 488
           F+ NLP+D+  E++++ F  FG V     V  + T + +G  F++F++ E+A  A+    
Sbjct: 119 FVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELN 178

Query: 489 TTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETN 526
                G  L+GR L V KA        +  +       
Sbjct: 179 -----GKELEGRPLRVQKAQPASQPRSELSNNLDASFA 211

Length = 306

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 25/58 (43%), Positives = 34/58 (58%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           + IRN+PF A   E+K++FS  G V    I  +  TG SKG AFVKF  K  A+  ++
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 24/60 (40%), Positives = 38/60 (63%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL + N+P+     E+K+ FS  G V +  +P + +TGLSKG+ FV F+ +   E+A+QK
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 52.0 bits (125), Expect = 1e-08
 Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L + NIPF+ +  +++ MF   G + +V I  N + G SKGF FV F    DA+ A +K
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFN-ERG-SKGFGFVTFANSADADRAREK 59

Query: 278 FNGQKFGKRPIAVDWA 293
            +G     R I V+ A
Sbjct: 60  LHGTVVEGRKIEVNNA 75

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 25/64 (39%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 235 DMFSPVG-LVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA 293
           D FS  G ++    I  + DTG SKGFAF+ +     +++AI+  NGQ    RPI V +A
Sbjct: 20  DTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPITVSYA 79

Query: 294 VPKN 297
             K+
Sbjct: 80  FKKD 83

This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 83

>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 21/64 (32%), Positives = 38/64 (59%)

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
            +++++FS  G +  V + ++  TG S+GF FV F    DA+ A ++ NG +   R I V
Sbjct: 14  RDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRV 73

Query: 291 DWAV 294
           D+++
Sbjct: 74  DYSI 77

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 51.4 bits (124), Expect = 2e-08
 Identities = 25/68 (36%), Positives = 33/68 (48%), Gaps = 1/68 (1%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           N+PF  +  E++  F   G V  V I  +  TG+ KGF +V F  K     A+ K NG K
Sbjct: 6   NLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KLNGIK 64

Query: 283 FGKRPIAV 290
              R I V
Sbjct: 65  LKGRKIRV 72

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 51.2 bits (122), Expect = 2e-08
 Identities = 26/63 (41%), Positives = 35/63 (55%)

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
            +IK  F+P G + +  +  +  TG SKG+ FV F  K DAE+AI    GQ  G R I  
Sbjct: 16  EDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRT 75

Query: 291 DWA 293
           +WA
Sbjct: 76  NWA 78

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 7/83 (8%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           N IFI  LP  L  ++VK+   +FG++ +F  V    T   KG  F ++        A+ 
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAI- 59

Query: 486 ASKTTSGL-GIFLKGRQLTVLKA 507
                +GL G+ L  ++LTV +A
Sbjct: 60  -----AGLNGMQLGDKKLTVQRA 77

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 50.1 bits (120), Expect = 4e-08
 Identities = 22/73 (30%), Positives = 40/73 (54%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+ F A  + I + F   G + +V +P + D+G  KGF +V+F+ +  A++A+   
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 279 NGQKFGKRPIAVD 291
            G     RP+ +D
Sbjct: 61  GGTDLLGRPVRLD 73

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 50.8 bits (122), Expect = 4e-08
 Identities = 20/66 (30%), Positives = 29/66 (43%)

Query: 224 IPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF 283
           +P  A    +K +FS  G V  V +P    TG  KGFAF++F    +A+ A +  N    
Sbjct: 7   LPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHLNNPPE 66

Query: 284 GKRPIA 289
                 
Sbjct: 67  TATDKP 72

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 50.4 bits (121), Expect = 4e-08
 Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 3/80 (3%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNV-YIPHNT--DTGLSKGFAFVKFTCKRDAESA 274
           +L I N+  +     +  +FS  G +    ++ H +    G  +G+ FV F  K +AE A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 275 IQKFNGQKFGKRPIAVDWAV 294
           ++  NG+    + + V WA 
Sbjct: 61  LKSLNGKTALGKKLVVRWAH 80

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 56.0 bits (135), Expect = 4e-08
 Identities = 62/290 (21%), Positives = 113/290 (38%), Gaps = 63/290 (21%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           ++N+        + D FS  G + +  +  + + G S+G+ FV F  +  A++AIQK NG
Sbjct: 93  VKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNG 151

Query: 281 QKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSE 340
                + + V   + K+                            + +A      +N   
Sbjct: 152 MLLNDKEVYVGRFIKKH----------------------------EREAAPLKKFTNLYV 183

Query: 341 KEDLPSNADFDEEV--DIARKVLNKLTSTTGSLPSLSDDSALVKG------NKEQDSDKT 392
           K       + D  V  D  R++  K    T S   + D S   +G       K +D+ K 
Sbjct: 184 K-------NLDPSVNEDKLRELFAKFGEIT-SAAVMKDGSGRSRGFAFVNFEKHEDAAKA 235

Query: 393 VNE--SAKVSDVS---KLNSSKSKPKSLKQTEGE---DELQ---------NTIFICNLPF 435
           V E    K+       KL   +++ ++ ++ E     +ELQ           +++ NL  
Sbjct: 236 VEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDD 295

Query: 436 DLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
            + +E++++ FS  GE+ S   V+       +G GF+ F   E A  AV+
Sbjct: 296 TVTDEKLRELFSECGEITS-AKVMLDEKGVSRGFGFVCFSNPEEANRAVT 344

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 50.2 bits (120), Expect = 5e-08
 Identities = 18/39 (46%), Positives = 27/39 (69%)

Query: 254 TGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW 292
           +G S+G+ FV F  ++DAE+AI + NG+  G RPI  +W
Sbjct: 37  SGRSRGYGFVSFRSQQDAENAINEMNGKWLGSRPIRCNW 75

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 50.0 bits (120), Expect = 5e-08
 Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 6/79 (7%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             +F+ NLP+D   E++   F   G   S   +  + T + KG  F++F T EA T A+ 
Sbjct: 1   FILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK 60

Query: 486 ASKTTSGLGIFLKGRQLTV 504
              T       LKGR++ V
Sbjct: 61  LHHTL------LKGRKINV 73

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 50.3 bits (121), Expect = 5e-08
 Identities = 25/83 (30%), Positives = 47/83 (56%), Gaps = 7/83 (8%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           N I++ ++  DL  +++K  F AFG++ S        T + KG GF++++  ++A  A++
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 486 ASKTTSGLGIF-LKGRQLTVLKA 507
           +      + +F L G+QL V KA
Sbjct: 61  S------MNLFDLGGQQLRVGKA 77

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 50.2 bits (120), Expect = 5e-08
 Identities = 26/81 (32%), Positives = 48/81 (59%), Gaps = 4/81 (4%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL +  +  +A   E++++FSP G V ++Y+  + +   S+G AFVK++ K  A++AI+ 
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKA 59

Query: 278 FNG---QKFGKRPIAVDWAVP 295
            NG    +   +P+ V +A P
Sbjct: 60  LNGVYTMRGCDQPLIVRFADP 80

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 49.6 bits (119), Expect = 8e-08
 Identities = 19/59 (32%), Positives = 35/59 (59%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           +FI +LP +  ++++ Q F+ FG V+S    + + T + K  GF+ +   E+A AA+ A
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKA 59

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 54.9 bits (132), Expect = 8e-08
 Identities = 59/280 (21%), Positives = 106/280 (37%), Gaps = 49/280 (17%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL + N+ F     E++ +F P G + +V +  + +TG SKGF F++F    +A+ A++ 
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSN 337
            NG +   RPI V                G         D+ +  +  D   +   + + 
Sbjct: 248 MNGFELAGRPIKV----------------GYAQDSTYLLDAANTFEDIDKQQQMGKNLNT 291

Query: 338 SSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESA 397
              ++ +              K+          +P     S +    K Q  D  ++ + 
Sbjct: 292 EEREQLM-------------EKLDRDDGDGGLLIPGT--GSKIALMQKLQ-RDGIIDPNI 335

Query: 398 KVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEE-----------VKQRF 446
                +   +  ++   +  T   + L  T  + +  FD   EE           VK+  
Sbjct: 336 PSRYATGALAIMARNSFVPST--NNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEEC 393

Query: 447 SAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           S +G VV     ++  TK   G  +LKF +V+AA AA  A
Sbjct: 394 SKYGGVV----HIYVDTKNSAGKIYLKFSSVDAALAAFQA 429

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 49.5 bits (119), Expect = 9e-08
 Identities = 19/72 (26%), Positives = 33/72 (45%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           + I ++P      E++  FS  G V  + +  +  TG SKG+AFV+F     A+   +  
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 279 NGQKFGKRPIAV 290
           N     +R +  
Sbjct: 62  NNYLLFERLLKC 73

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 49.4 bits (118), Expect = 9e-08
 Identities = 22/73 (30%), Positives = 40/73 (54%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++ + +I F+   + I+  FSP G + ++ +  +  T   KGFAFV++     A+ A+++
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 278 FNGQKFGKRPIAV 290
            NG   G R I V
Sbjct: 62  MNGVMLGGRNIKV 74

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 49.1 bits (118), Expect = 1e-07
 Identities = 16/43 (37%), Positives = 26/43 (60%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
          +V  K + + +GF +V+F   EDA +A+E  NG  + GR + V
Sbjct: 31 LVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 5/84 (5%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T+F+ NLP+D  +E++++ FS  G +     V  + +K+ +G G++ F   E A  A+  
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 487 SKTTSGLGIFLKGRQLTVLKALDK 510
            K T        GR++ V  A  K
Sbjct: 61  KKKTK-----FGGRKIHVEFAKKK 79

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 49.1 bits (118), Expect = 1e-07
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 7/75 (9%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +++ NLP  +  E++++ FS +G+V     V ++   RP+G  F++F + E A AA+   
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58

Query: 488 KTTSGLGIFLKGRQL 502
                 G+ L GR L
Sbjct: 59  N-----GLVLDGRTL 68

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 49.1 bits (118), Expect = 1e-07
 Identities = 19/60 (31%), Positives = 32/60 (53%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +FI  L +D   E +++ FS +GEVV  V +   +T R +G GF+ F    +    ++A 
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 7/78 (8%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T+F+ NL +  + +++++ F   GEVV  V +      R KG G ++F T E A  A+  
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVD-VRIAQDDDGRSKGFGHVEFATEEGAQKALEK 59

Query: 487 SKTTSGLGIFLKGRQLTV 504
           S      G  L GR++ V
Sbjct: 60  S------GEELLGREIRV 71

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 5/81 (6%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T+F+ NL + +D+E +K  F  FG VV    +  + T R +G G++ F++ E A  A+ A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 487 SKTTSGLGIFLKGRQLTVLKA 507
                     L GR + V  +
Sbjct: 61  MDGKE-----LDGRPINVDFS 76

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|241121 cd12677, RRM4_Nop4p, RNA recognition motif 4 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 51.1 bits (122), Expect = 1e-07
 Identities = 35/110 (31%), Positives = 52/110 (47%), Gaps = 28/110 (25%)

Query: 574 HVSRTRLVIYNLPKSMTEKGLKKLCIDAVV-------------------SRASKQKPVIK 614
           H+S TRL I N+P+ +  K LK L   A+                    +R    +    
Sbjct: 1   HLSLTRLSIRNIPRHIDPKILKMLARQAIRGFADDVKKGLRAPLSKEEENRDKGHRYKEA 60

Query: 615 QIKFLQS---LKKGKVDTKH------YSRGVAFVEFTEHQHALVALRVLN 655
           Q+K  +S   +K+ KV+T+        SRG  F+EF  H++AL+ALR LN
Sbjct: 61  QLKKGKSGGVVKQAKVETEKAGSTAGRSRGYGFMEFISHKYALMALRWLN 110

This subgroup corresponds to the RRM4 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 156

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 48.1 bits (115), Expect = 2e-07
 Identities = 25/78 (32%), Positives = 45/78 (57%), Gaps = 2/78 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+ + A+ +++++ F   G V +V I  + D G SKGF  V+F  +  A+ A++K 
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEFATEEGAQKALEK- 59

Query: 279 NGQKFGKRPIAVDWAVPK 296
           +G++   R I VD A  +
Sbjct: 60  SGEELLGREIRVDLATER 77

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 25/78 (32%), Positives = 40/78 (51%)

Query: 216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           K  LI+  +P     +EI+ +FS +G + +  +  +  TG S G+ FV +    DAE AI
Sbjct: 1   KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

Query: 276 QKFNGQKFGKRPIAVDWA 293
              NG +   + I V +A
Sbjct: 61  NTLNGLRLQNKTIKVSYA 78

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 48.4 bits (115), Expect = 2e-07
 Identities = 18/59 (30%), Positives = 35/59 (59%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           +++ NLP  L  +E+++ F A+G +V    +  + T  P+G  F+++   E A AA+S+
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 48.0 bits (115), Expect = 3e-07
 Identities = 29/81 (35%), Positives = 40/81 (49%), Gaps = 13/81 (16%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVS-FVPVLHQVTKRPKGTGFLKFKTVEAATAA 483
           +  +F+ NLP D+  EE K+ FS +GEV   F+        + KG GF++  T   A  A
Sbjct: 1   RCRLFVGNLPNDITEEEFKELFSKYGEVSEVFLN-------KEKGFGFIRLDTRTNAEKA 53

Query: 484 VSASKTTSGLGIFLKGRQLTV 504
            +        GI  KGRQL V
Sbjct: 54  KAELD-----GIMRKGRQLRV 69

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 48.4 bits (116), Expect = 3e-07
 Identities = 23/71 (32%), Positives = 37/71 (52%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           I  +P++    +I  +FS  G + ++ +  +  TG SKGFAF+ +  +R    A+   NG
Sbjct: 14  IGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNG 73

Query: 281 QKFGKRPIAVD 291
            K   R I VD
Sbjct: 74  IKLLGRTIRVD 84

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 47.8 bits (114), Expect = 3e-07
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
             + + FS  G +  V IP + +TG SKGFA+++F      E A++  +G   G   + V
Sbjct: 18  RSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALE-LDGSDLGGGNLVV 76

Query: 291 D 291
           D
Sbjct: 77  D 77

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 48.0 bits (115), Expect = 4e-07
 Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 3/72 (4%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWN---VYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           ++IRNIP K     +  +    G       +Y+P +     + G+AF+ F     AE   
Sbjct: 1   VMIRNIPNKYTQEMLLQLLDEHGKGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEKFY 60

Query: 276 QKFNGQKFGKRP 287
           + FNG+K+    
Sbjct: 61  KAFNGKKWKNFK 72

This subfamily corresponds to the RRM3 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 86

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 47.8 bits (114), Expect = 4e-07
 Identities = 21/69 (30%), Positives = 35/69 (50%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L IRN+ +     +++ +FS  G +  V++P +  T   KGFAFV +     A  A  +
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 278 FNGQKFGKR 286
            +G  F  R
Sbjct: 64  LDGTVFQGR 72

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 49.7 bits (118), Expect = 4e-07
 Identities = 30/107 (28%), Positives = 49/107 (45%), Gaps = 5/107 (4%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL I  + +      ++D F+  G V +  +  + +TG S+GF FV F  +  A +AI +
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 278 FNGQKFGKRPIAVDWA-----VPKNIYSSGGAAAGVQNKGDGNSDSG 319
            +G++   R I V+ A      P+     GG + G    G G    G
Sbjct: 96  MDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGGGGDGGG 142

Length = 144

>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 47.2 bits (113), Expect = 5e-07
 Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 6/78 (7%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           ++F+ NLPFD++ EE+++ F   G+V +   V  + T   KG G++ FKT ++   A+  
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL 60

Query: 487 SKTTSGLGIFLKGRQLTV 504
           +      GI LKGR++ V
Sbjct: 61  N------GIKLKGRKIRV 72

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 47.3 bits (113), Expect = 5e-07
 Identities = 21/75 (28%), Positives = 38/75 (50%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           LI+  +P      E++ +F  +G + +  I  +  TG S G+ FV +  + DA+ AI   
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 279 NGQKFGKRPIAVDWA 293
           NG +   + + V +A
Sbjct: 63  NGFEIRNKRLKVSYA 77

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 47.5 bits (113), Expect = 5e-07
 Identities = 25/76 (32%), Positives = 37/76 (48%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL I  + F      ++ +FS  G +  V +  + +T  S+GF FV F    DA+ A+  
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 278 FNGQKFGKRPIAVDWA 293
            NG+    R I VD A
Sbjct: 62  MNGKSVDGRQIRVDQA 77

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 47.3 bits (113), Expect = 5e-07
 Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 5/78 (6%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +RNI    +  E++ +F   G +  +Y          +GF  V +   R A  A +  
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRTLY-----TACKHRGFIMVSYYDIRAARRAKRAL 58

Query: 279 NGQKFGKRPIAVDWAVPK 296
            G + G R + + +++PK
Sbjct: 59  QGTELGGRKLDIHFSIPK 76

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 47.2 bits (113), Expect = 6e-07
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L I ++P +    ++  +F+P G V +  +  + +TG SK F FV +     A++AI+  
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 279 NG-QKFGKR 286
           NG Q  GKR
Sbjct: 61  NGFQVGGKR 69

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 47.4 bits (112), Expect = 7e-07
 Identities = 26/80 (32%), Positives = 38/80 (47%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           W + + N+   A  + +  MF P G V NV +  + +T   KGF FV  T   +A  AI 
Sbjct: 4   WCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIA 63

Query: 277 KFNGQKFGKRPIAVDWAVPK 296
             NG + G R + V +   K
Sbjct: 64  SLNGYRLGDRVLQVSFKTNK 83

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 46.6 bits (111), Expect = 9e-07
 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+P+     ++   F   G   +V +  +  TG SKG AFV+F        A++  
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 279 NGQKFGKRPIAVD 291
                  R I V+
Sbjct: 63  -HTLLKGRKINVE 74

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 46.6 bits (111), Expect = 9e-07
 Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           +K KL +  +PF     E++ +F   G+V +V +  N  +G  KG A+V++  +  A  A
Sbjct: 1   EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQA 59

Query: 275 IQKFNGQKFGKRPIAV 290
           + K +G +  ++ I+V
Sbjct: 60  VLKMDGTEIKEKTISV 75

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding protein PIN4, fission yeast RNA-binding post-transcriptional regulators cip1, cip2 and similar proteins

 Score = 46.7 bits (111), Expect = 9e-07
 Identities = 18/74 (24%), Positives = 40/74 (54%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           ++I+NIPF  +  ++ D+   +G+       ++ D G+ +G AF  F    +A++ ++  
Sbjct: 4   IVIKNIPFSLRKEQLLDIIEDLGIPLPYAFNYHFDNGVFRGLAFANFRSPEEAQTVVEAL 63

Query: 279 NGQKFGKRPIAVDW 292
           NG +   R + V++
Sbjct: 64  NGYEISGRRLRVEY 77

This subfamily corresponds to the RRM in PIN4, also termed psi inducibility protein 4 or modifier of damage tolerance Mdt1, a novel phosphothreonine (pThr)-containing protein that specifically interacts with the pThr-binding site of the Rad53 FHA1 domain. It is encoded by gene MDT1 (YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is involved in normal G2/M cell cycle progression in the absence of DNA damage and functions as a novel target of checkpoint-dependent cell cycle arrest pathways. It contains an N-terminal RRM, a nuclear localization signal, a coiled coil, and a total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein 1) and cip2 (Csx1-interacting protein 2) are novel cytoplasmic RRM-containing proteins that counteract Csx1 function during oxidative stress. They are not essential for viability in fission yeast Schizosaccharomyces pombe. Both cip1 and cip2 contain one RRM. Like PIN4, Cip2 also possesses an R3H motif that may function in sequence-specific binding to single-stranded nucleic acids. . Length = 79

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 46.5 bits (111), Expect = 9e-07
 Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 15/79 (18%)

Query: 578 TRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVA 637
           +RL++ NLP S+TE  LK+          SK    I  +K L++ + GK      SR +A
Sbjct: 1   SRLIVKNLPASLTEAELKEH--------FSKHGGEITDVKLLRT-EDGK------SRRIA 45

Query: 638 FVEFTEHQHALVALRVLNN 656
           F+ +   + A  A    NN
Sbjct: 46  FIGYKTEEEAQKAKDYFNN 64

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 46.6 bits (110), Expect = 9e-07
 Identities = 24/80 (30%), Positives = 41/80 (51%)

Query: 216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           +  LI+  +P     +E++ +FS +G V +  +  +   G S G+ FV +   +DAE AI
Sbjct: 1   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAI 60

Query: 276 QKFNGQKFGKRPIAVDWAVP 295
              NG +   + I V +A P
Sbjct: 61  NTLNGLRLQSKTIKVSYARP 80

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 46.4 bits (110), Expect = 9e-07
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 10/73 (13%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           N  + A+ +EI+ +F   G V  V         +  GFAFV    +RDAE AI+  +  +
Sbjct: 7   NFEYDARQSEIERLFGKYGRVDRV--------DMKSGFAFVYMEDERDAEDAIRGLDNFE 58

Query: 283 FG--KRPIAVDWA 293
           FG  +R + V+WA
Sbjct: 59  FGRQRRRLRVEWA 71

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 46.6 bits (110), Expect = 9e-07
 Identities = 28/86 (32%), Positives = 43/86 (50%), Gaps = 3/86 (3%)

Query: 210 EGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKR 269
           E SKT    LI+  +P      E+K +F  +G + +  +  +  TG S G+ FV +   +
Sbjct: 1   EDSKTN---LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPK 57

Query: 270 DAESAIQKFNGQKFGKRPIAVDWAVP 295
           DAE AI   NG +   + I V +A P
Sbjct: 58  DAEKAINTLNGLRLQTKTIKVSYARP 83

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 46.4 bits (111), Expect = 9e-07
 Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L + N+ +     +++++F  VG V  V I ++  +G S+G A V F  + DAE AI++
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQ 60

Query: 278 FNGQKFGKRPIAV 290
           FNG     +P+ V
Sbjct: 61  FNGVLLDGQPMQV 73

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 51.1 bits (122), Expect = 9e-07
 Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 7/94 (7%)

Query: 216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           K  LI+  +P      EI+ +F+ +G + +  +  +  TG S G+ FV +    DAE A+
Sbjct: 3   KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAV 62

Query: 276 QKFNGQKFGKRPIAVDWAVPK-------NIYSSG 302
              NG +   + I V +A P        N+Y SG
Sbjct: 63  NSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSG 96

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 19/46 (41%), Positives = 28/46 (60%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          ++T + +   RGFG+V+    E+AN A+E  NGT  GGR + V  A
Sbjct: 31 VITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGGRTLTVNEA 76

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMFS-PVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           +LI++N+P      E+K+ FS   G + +V +    D G S+  AF+ +  + +A+ A  
Sbjct: 2   RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTED-GKSRRIAFIGYKTEEEAQKAKD 60

Query: 277 KFNGQKFGKRPIAVDWA 293
            FN        I+V++A
Sbjct: 61  YFNNTYINTSKISVEFA 77

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 229 KVNE--IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKR 286
           KV E  + ++F   G V NV+IP +  T   +G+ FV+F  + DA+ AI+  N  K   +
Sbjct: 9   KVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNMIKLYGK 68

Query: 287 PIAV 290
           PI V
Sbjct: 69  PIRV 72

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 16/76 (21%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
             ++ +  IP     +E+  +F   G ++ + +  +   GL++G+AFV +T K  A+ A+
Sbjct: 1   GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFS-GLNRGYAFVTYTNKEAAQRAV 59

Query: 276 QKFNGQKFGK-RPIAV 290
           ++ +  +    + + V
Sbjct: 60  KQLHNYEIRPGKRLGV 75

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 22/60 (36%), Positives = 34/60 (56%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T+++ NLPF L N ++ + FS +G+VV    V  + T++ KG  F+ F   E A   V A
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 46.2 bits (109), Expect = 1e-06
 Identities = 25/80 (31%), Positives = 38/80 (47%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           W + + N+  +A  + +  +F P G V NV +  +  T   KGF FV  T   +A  AI 
Sbjct: 2   WCIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIA 61

Query: 277 KFNGQKFGKRPIAVDWAVPK 296
             NG + G R + V +   K
Sbjct: 62  SLNGYRLGDRVLQVSFKTSK 81

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 46.1 bits (109), Expect = 1e-06
 Identities = 22/65 (33%), Positives = 40/65 (61%)

Query: 232 EIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD 291
           +++++FS  G +  V + ++  TG S+GFAFV F    D++ A++  NG +   R I VD
Sbjct: 15  DLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRVD 74

Query: 292 WAVPK 296
           +++ K
Sbjct: 75  YSITK 79

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 17/34 (50%), Positives = 23/34 (67%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVK 44
          +GFG V F   EDA RA+EM NG  + GR++ V+
Sbjct: 39 KGFGTVLFESPEDAQRAIEMFNGYDLEGRELEVR 72

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 45.9 bits (109), Expect = 2e-06
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 5/77 (6%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +++ ++ F+L  + ++Q FS FG + S       VT + KG  F++++  EAA  A+   
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 488 KTTSGLGIFLKGRQLTV 504
                 G+ L GR + V
Sbjct: 63  N-----GVMLGGRNIKV 74

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 46.0 bits (109), Expect = 2e-06
 Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 5/80 (6%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +FI  L FD + + ++Q FS +G++   V V  + T+R +G GF+ F+  + A  A+ A 
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 488 KTTSGLGIFLKGRQLTVLKA 507
              S     + GRQ+ V +A
Sbjct: 63  NGKS-----VDGRQIRVDQA 77

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 6/61 (9%)

Query: 232 EIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD 291
           E++ +F P G +  V IP        KG  FV+F  +  AE+AIQ+  G   G   I + 
Sbjct: 17  ELRSLFGPFGEIVYVKIP------PGKGCGFVQFVHRAAAEAAIQQLQGTIIGGSRIRLS 70

Query: 292 W 292
           W
Sbjct: 71  W 71

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           ++++N+PF     E++++F   G +  + +P       S+  A V+F    DA  A +  
Sbjct: 3   ILVKNLPFGTTEEELRELFEKFGSLGRLLLPP------SRTIALVEFLEPSDARKAFKSL 56

Query: 279 NGQKFGKRPIAVDWA 293
             ++F   P+ ++WA
Sbjct: 57  AYKRFKHVPLYLEWA 71

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           T+F+ NL + +  +E+++ FS  GE+     V +    + KG  +++F+  E+   A+ 
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALK 58

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 5/76 (6%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ + N+  +A   E++D F   G + +V++  N       GFAFV+F   RDAE A++ 
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRA 55

Query: 278 FNGQKFGKRPIAVDWA 293
            +G++     + V+ +
Sbjct: 56  LDGRRICGNRVRVELS 71

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 45.8 bits (108), Expect = 2e-06
 Identities = 26/81 (32%), Positives = 38/81 (46%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           W + I N+   A    +  MF P G V NV +  + +T   KGF FV  T   +A  AI 
Sbjct: 2   WCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIA 61

Query: 277 KFNGQKFGKRPIAVDWAVPKN 297
             NG + G + + V +   K+
Sbjct: 62  SLNGYRLGDKILQVSFKTSKS 82

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 45.6 bits (109), Expect = 2e-06
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 230 VNE--IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRP 287
           V E  + ++FSP G V ++ +  +  T  S G+A+V F    DAE A+   N      +P
Sbjct: 11  VTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLNFDVIKGKP 70

Query: 288 IAVDW 292
           I + W
Sbjct: 71  IRIMW 75

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 20/36 (55%), Positives = 25/36 (69%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          +GFG+V FA   DA+RA E  +GT V GRKI V +A
Sbjct: 40 KGFGFVTFANSADADRAREKLHGTVVEGRKIEVNNA 75

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 18/45 (40%), Positives = 26/45 (57%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          +T + +   RGFGYV F   EDA +A+E  +G  + GR I V  +
Sbjct: 32 ITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 45.4 bits (108), Expect = 3e-06
 Identities = 28/80 (35%), Positives = 40/80 (50%), Gaps = 6/80 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           IF+  LP D+  EE K+ FS FG+VV    +    T R +G GF+ F +  A     SA 
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 488 KTTSGLGIFLKGRQLTVLKA 507
                  + L G+Q+ V +A
Sbjct: 62  ------MLELGGKQVEVKRA 75

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 6/85 (7%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             +++ NL  D+D+E++K+ F  +G++ S   V+     + KG GF+ F+  EAA  AV 
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAK-VMKDDEGKSKGFGFVNFENHEAAQKAVE 60

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDK 510
                   G  + G++L V +A  K
Sbjct: 61  ELN-----GKEVNGKKLYVGRAQKK 80

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 45.1 bits (106), Expect = 3e-06
 Identities = 24/82 (29%), Positives = 40/82 (48%)

Query: 216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           K  LI+  +P      E + +F  +G + +  +  +  TG S G+ FV +   +DAE AI
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 276 QKFNGQKFGKRPIAVDWAVPKN 297
              NG +   + I V +A P +
Sbjct: 62  NTLNGLRLQTKTIKVSYARPSS 83

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 6/77 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           + + NLPF     ++K+ FS FG V   V +  +   + KG  F++F +   A  A+   
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWE-VTIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 488 KTTSGLGIFLKGRQLTV 504
                    +KGR + V
Sbjct: 61  NGKK-----IKGRPVAV 72

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 15/41 (36%), Positives = 24/41 (58%)

Query: 4  KKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVK 44
          +    + +GF +V+F   EDA +A+E  NG  + GRK+ V 
Sbjct: 32 RDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 8/83 (9%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSF-VPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
             + + N+PF+   +E+++ FS FG+V S  +P   +     +G  F++F T + A  A+
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPK--KFDGSHRGFAFVEFVTKQEAQNAM 58

Query: 485 SASKTTSGLGIFLKGRQLTVLKA 507
            A K+T      L GR L +  A
Sbjct: 59  EALKSTH-----LYGRHLVLEYA 76

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 45.1 bits (107), Expect = 4e-06
 Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +FI NL +    E++++ FS +G +      + ++TK+PKG  F+ +   E A  A +  
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 488 KTTSGLGIFLKGRQLTVLKA 507
             T       +GR L +L +
Sbjct: 65  DGTV-----FQGRLLHLLPS 79

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 45.0 bits (107), Expect = 4e-06
 Identities = 22/73 (30%), Positives = 36/73 (49%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           + N+PF    N++  +FS  G V  V I  + +T  SKG AF+ F  + DA   ++  N 
Sbjct: 6   VSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNN 65

Query: 281 QKFGKRPIAVDWA 293
           ++   R +    A
Sbjct: 66  KELFGRTLKCSIA 78

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 45.0 bits (106), Expect = 4e-06
 Identities = 22/75 (29%), Positives = 40/75 (53%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +RN+    +  +++  F   G + +VY+P +  T   +GFA+++F   RDAE A+   
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 279 NGQKFGKRPIAVDWA 293
           N +    R I + +A
Sbjct: 63  NRKWVCGRQIEIQFA 77

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
            +  K +  ++ + FS  G V +V I  + ++  SKG A+V+F  +     A+    GQ+
Sbjct: 6   QLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-LTGQR 64

Query: 283 FGKRPIAV 290
              +PI V
Sbjct: 65  LLGQPIMV 72

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 45.1 bits (106), Expect = 4e-06
 Identities = 25/82 (30%), Positives = 39/82 (47%)

Query: 216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           K  LI+  +P      E K +F  +G + +  +  +  TG S G+ FV +    DA+ AI
Sbjct: 3   KTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAI 62

Query: 276 QKFNGQKFGKRPIAVDWAVPKN 297
              NG K   + I V +A P +
Sbjct: 63  NTLNGLKLQTKTIKVSYARPSS 84

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 20/52 (38%), Positives = 26/52 (50%)

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
             I   F+  G V +V I  N  TG S G+ FV+F     AE A+Q  NG+ 
Sbjct: 14  AYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKP 65

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           + N+ +     E+++ F   G +  + I  +  TG  KGFA+++F  K   E+A+   N 
Sbjct: 4   VGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-LNE 62

Query: 281 QKFGKRPIAV 290
            +F  R I V
Sbjct: 63  SEFRGRQIKV 72

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 15/78 (19%)

Query: 579 RLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAF 638
            L + NLP   TE+ L++L           +   ++ ++ ++  + GK      S+G AF
Sbjct: 1   TLFVGNLPPDTTEEELRELF---------SKFGKVESVRLVRDKETGK------SKGFAF 45

Query: 639 VEFTEHQHALVALRVLNN 656
           VEF   + A  AL  LN 
Sbjct: 46  VEFESEEDAEKALEALNG 63

Length = 73

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 44.7 bits (106), Expect = 5e-06
 Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 2/61 (3%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPV-LHQVTKRPKGTGFLKFKTVEAATAAVS 485
           T+++  LP +  +E +K  FS +G VV +V +  ++ T   KG  F++F+T E A  A  
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVV-YVSLPRYKHTGDIKGFAFIEFETPEEAQKACK 59

Query: 486 A 486
            
Sbjct: 60  H 60

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 44.7 bits (106), Expect = 5e-06
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 6/80 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           IF+  LP ++   ++++ FS FG V   V +     KRP+G GF+ F++ ++    V+  
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEH 64

Query: 488 KTTSGLGIFLKGRQLTVLKA 507
                    + G+++ V +A
Sbjct: 65  FHD------INGKKVEVKRA 78

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 20/53 (37%), Positives = 34/53 (64%), Gaps = 2/53 (3%)

Query: 230 VNE--IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           VN+  +K++FS  G V +V +P + +  L +G+A+V+F    DAE AI+  +G
Sbjct: 10  VNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDG 62

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 6/70 (8%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           N+P      E++  FSP G +  V +  +      KG+AFV+F     A +AI   NG  
Sbjct: 7   NLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVAVNGTS 60

Query: 283 FGKRPIAVDW 292
              + +   W
Sbjct: 61  INGQTVKCSW 70

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 44.6 bits (105), Expect = 5e-06
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL + ++P      E++ MF   G V  V I  +  TG  +G  FVK++ + +A+ AI+ 
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 278 FNGQKF---GKRPIAVDWA 293
            + Q+    G  P+ V +A
Sbjct: 61  LHNQRTLPGGASPVQVRYA 79

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 44.5 bits (106), Expect = 6e-06
 Identities = 18/40 (45%), Positives = 25/40 (62%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          + E RGFG+V F  +EDA+ A+   NG  + GR I V+ A
Sbjct: 39 TGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKVEKA 78

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240959 cd12515, RRM5_RBM12_like, RNA recognition motif 5 in RNA-binding protein RBM12, RBM12B and similar proteins

 Score = 44.4 bits (105), Expect = 6e-06
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 4/72 (5%)

Query: 221 IRNIPFKAKVNEIKDMFS--PVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           ++N+PF A + EI D F    V +  +V + +N D G   G A V F   R+A +A+++ 
Sbjct: 5   VQNLPFTATIEEILDFFYGYRV-IPGSVSLLYN-DNGAPTGEATVAFDTHREAMAAVREL 62

Query: 279 NGQKFGKRPIAV 290
           NG+  G R + +
Sbjct: 63  NGRPIGTRKVKL 74

This subfamily corresponds to the RRM5 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. . Length = 75

>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 44.6 bits (105), Expect = 6e-06
 Identities = 22/65 (33%), Positives = 40/65 (61%)

Query: 232 EIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD 291
           +++++FS  G + +V I ++  +  S+GFAFV F    DA+ A ++ NG +   R I VD
Sbjct: 25  DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 84

Query: 292 WAVPK 296
           +++ K
Sbjct: 85  FSITK 89

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 44.2 bits (104), Expect = 6e-06
 Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++ +RN+PF      +KD F+  G V  +Y     + G SKG   V+F     AE A + 
Sbjct: 1   QIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVRFESPEVAERACRM 58

Query: 278 FNGQKFGKRPIAV 290
            NG K   R I V
Sbjct: 59  MNGYKLNGREIDV 71

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 43.7 bits (104), Expect = 7e-06
 Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 16/77 (20%)

Query: 580 LVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFV 639
           L + NLP   TE+ LK L           +   I+ I+          D    S+G AFV
Sbjct: 1   LFVGNLPPDTTEEDLKDLF---------SKFGPIESIRI-------VRDETGRSKGFAFV 44

Query: 640 EFTEHQHALVALRVLNN 656
           EF + + A  AL  LN 
Sbjct: 45  EFEDEEDAEKALEALNG 61

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 45.8 bits (108), Expect = 7e-06
 Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 5/87 (5%)

Query: 424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAA 483
           +   +FI  L +  D+  ++  F+ FG+VV    ++ + T R +G GF+ F    AATAA
Sbjct: 33  MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAA 92

Query: 484 VSASKTTSGLGIFLKGRQLTVLKALDK 510
           +S        G  L GR + V  A D+
Sbjct: 93  ISEMD-----GKELNGRHIRVNPANDR 114

Length = 144

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 44.2 bits (104), Expect = 8e-06
 Identities = 21/75 (28%), Positives = 37/75 (49%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L I N+P      + +++  P G +   ++ ++  TG SKG+ FV++  K  A  A    
Sbjct: 2   LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61

Query: 279 NGQKFGKRPIAVDWA 293
            G++ G R + V W 
Sbjct: 62  LGKQLGSRTLYVHWT 76

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 44.2 bits (105), Expect = 8e-06
 Identities = 18/61 (29%), Positives = 36/61 (59%), Gaps = 2/61 (3%)

Query: 232 EIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK--RPIA 289
           ++++ F+P G + ++++  +  T  SKG A+VKF     A  A+++ NG+  G   +P+ 
Sbjct: 18  DLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDTKPLK 77

Query: 290 V 290
           V
Sbjct: 78  V 78

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 43.8 bits (104), Expect = 9e-06
 Identities = 14/40 (35%), Positives = 23/40 (57%)

Query: 4  KKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
          +K   + +GF +VQF    DA +A++  NG  + GR + V
Sbjct: 33 RKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRPVAV 72

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 43.5 bits (103), Expect = 9e-06
 Identities = 21/61 (34%), Positives = 34/61 (55%)

Query: 233 IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW 292
           +K  F   G V    +  + +TG S+GF +V F    DA+ AI+  +G++   RPI VD+
Sbjct: 16  LKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDF 75

Query: 293 A 293
           +
Sbjct: 76  S 76

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 14/40 (35%), Positives = 25/40 (62%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKI 41
          + +  +   +GF +V+F   EDA +A+E  NG  +GGR++
Sbjct: 30 IVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 6/85 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQV-TKRPKGTGFLKFKTVEAATAAVSA 486
           +FI NL  ++D + +   FSAFG ++    ++    T   KG  F+ + + EA+ AA+ A
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 487 SKTTSGLGIFLKGRQLTVLKALDKK 511
                  G +L  R +TV  A  K 
Sbjct: 64  MN-----GQYLCNRPITVSYAFKKD 83

This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 83

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 19/46 (41%), Positives = 26/46 (56%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          +V  + +   RGFG+V F   +DA  A+   NG SV GR+I V  A
Sbjct: 32 VVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRVDQA 77

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 43.9 bits (103), Expect = 1e-05
 Identities = 24/80 (30%), Positives = 38/80 (47%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           W + + N+   +  + +  +F P G V NV +  + +T   KGF FV  T   +A  AI 
Sbjct: 4   WCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIA 63

Query: 277 KFNGQKFGKRPIAVDWAVPK 296
             NG + G R + V +   K
Sbjct: 64  SLNGYRLGDRVLQVSFKTNK 83

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL++ N+ F    ++IK++F+  G +    + H   +G S G A V F  + DA  A+++
Sbjct: 2   KLLVSNLDFGVSDDDIKELFAEFGALKKAAV-HYDRSGRSLGTADVVFERRADALKAMKQ 60

Query: 278 FNGQKFGKRP 287
           +NG     RP
Sbjct: 61  YNGVPLDGRP 70

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 7/85 (8%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           N IF+  +P D   EE++  FS FG V   V ++       KG GF+ F+T E A   ++
Sbjct: 3   NRIFVGGIPPDTTEEELRDFFSRFGSVKD-VKIITDRAGVSKGYGFVTFETQEDAEKILA 61

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDK 510
                    +  +G++L +  A+ K
Sbjct: 62  MGN------LNFRGKKLNIGPAIRK 80

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 15/59 (25%), Positives = 32/59 (54%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           +++  LP  +  +E++Q FS +G +++   +  Q+T   +G GF++F     A  A+  
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 13/85 (15%)

Query: 432 NLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTS 491
            LP+    +++K  FS FGE++         T + KG GF++F   E     +S      
Sbjct: 6   GLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQRH--- 62

Query: 492 GLGIFLKGRQLTVLKALDKKLAHDK 516
                + GR   V      K+ + K
Sbjct: 63  ----MIDGRWCDV------KIPNSK 77

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 15/62 (24%), Positives = 32/62 (51%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             +F+  L     +  +++ F+ +G++   V ++   TKR +G GF+ F + + A  A+ 
Sbjct: 3   CKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

Query: 486 AS 487
           A 
Sbjct: 63  AQ 64

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 8/86 (9%)

Query: 212 SKTQKWKLIIRNIP--FKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKR 269
           S+     L +  +P  F+  V+ ++ +FS VG      +    + G  +GFAFV++    
Sbjct: 2   SRC----LFVDRLPKTFR-DVSILRKLFSQVGKPTFCQLAIAPN-GQPRGFAFVEYATAE 55

Query: 270 DAESAIQKFNGQKFGKRPIAVDWAVP 295
           DAE A Q  NG      PI V +  P
Sbjct: 56  DAEEAQQALNGHSLQGSPIRVSFGNP 81

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 23/75 (30%), Positives = 40/75 (53%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +RNI    +  +++  F   G + +VY+P +  T   +GFA+V+F   RDAE A+   
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 279 NGQKFGKRPIAVDWA 293
           + +    R I + +A
Sbjct: 63  DRKWICGRQIEIQFA 77

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 43.3 bits (103), Expect = 1e-05
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPH---NTDTGLSKGFAFVKFTCKRDAESAI 275
           L + N P     ++I+D+F   G + ++  P    N     ++ F +V+FT    A +A+
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNK----TRRFCYVQFTSPESAAAAV 58

Query: 276 QKFNGQKFGKRPIAVD 291
              NG+      + V 
Sbjct: 59  ALLNGKLGEGYKLVVK 74

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 16/59 (27%), Positives = 29/59 (49%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           K+ +  +P+    + ++  FS  G +    +  +  TG S+G+ FV F  K  AE A +
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 47.5 bits (113), Expect = 2e-05
 Identities = 29/73 (39%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 2   VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIG----VKHAMHRASLEQRRS 57
           V K GS   RGF +V F   EDA +AVE  NG  +G  K G    V  A  RA  E    
Sbjct: 210 VMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELR 269

Query: 58  KVTQEVQAEDIEK 70
           +  +E+Q E   K
Sbjct: 270 RKFEELQQERKMK 282

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 47.5 bits (113), Expect = 2e-05
 Identities = 22/85 (25%), Positives = 45/85 (52%), Gaps = 1/85 (1%)

Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDA 271
            K Q   L ++N+       +++++FS  G + +  +  + + G+S+GF FV F+   +A
Sbjct: 281 MKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEA 339

Query: 272 ESAIQKFNGQKFGKRPIAVDWAVPK 296
             A+ + +G+  G +P+ V  A  K
Sbjct: 340 NRAVTEMHGRMLGGKPLYVALAQRK 364

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 47.1 bits (112), Expect = 2e-05
 Identities = 58/283 (20%), Positives = 105/283 (37%), Gaps = 78/283 (27%)

Query: 375 SDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLP 434
           S  +A+ K N    +DK V     V         +   K  ++     +  N +++ NL 
Sbjct: 141 SAKAAIQKVNGMLLNDKEV----YVG--------RFIKKHEREAAPLKKFTN-LYVKNLD 187

Query: 435 FDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLG 494
             ++ +++++ F+ FGE+ S   V+   + R +G  F+ F+  E A  AV          
Sbjct: 188 PSVNEDKLRELFAKFGEITSAA-VMKDGSGRSRGFAFVNFEKHEDAAKAVEE-------- 238

Query: 495 IFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDM 554
                              + K+I              LAKEG  L    A +    +  
Sbjct: 239 ------------------MNGKKIG-------------LAKEGKKLYVGRAQKRAEREAE 267

Query: 555 --SKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPV 612
              K + L +++  K Q  N       L + NL  ++T++ L++L           +   
Sbjct: 268 LRRKFEELQQERKMKAQGVN-------LYVKNLDDTVTDEKLREL---------FSECGE 311

Query: 613 IKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLN 655
           I   K +       +D K  SRG  FV F+  + A  A+  ++
Sbjct: 312 ITSAKVM-------LDEKGVSRGFGFVCFSNPEEANRAVTEMH 347

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +  +P      E++ +FS  G +    I  +  TG+S+G  F++F  + +AE AI+  
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 279 NGQK--FGKRPIAVDWA 293
           NGQK      PI V +A
Sbjct: 63  NGQKPEGASEPITVKFA 79

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 13/84 (15%)

Query: 221 IRNIPFKAKVNEIKDM---FSPVGLVWNVYIPHNTDTGLSK------GFAFVKFTCKRDA 271
           I N+ + +   ++++    F PV    +V IP  T  G         G A+ +F+    A
Sbjct: 4   ISNLSYSSSEEDLEEFLKDFEPV----SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 272 ESAIQKFNGQKFGKRPIAVDWAVP 295
           E  ++  NG+ F  R + V   VP
Sbjct: 60  EKVVKDLNGKVFKNRKLFVKLHVP 83

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 42.9 bits (102), Expect = 2e-05
 Identities = 23/59 (38%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           IFI NL   +DN+ +   FSAFG ++S      +     KG GF+ F+T EAA  A+  
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGG-SKGYGFVHFETEEAAVRAIEK 62

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +LI++N+P   K ++++ +F   G + +V + +  D G  + F FV +  + +A+ A++ 
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKALKH 60

Query: 278 FNGQKFGKRPIAVD 291
           FN        I V+
Sbjct: 61  FNNSFIDTSKITVE 74

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 8/79 (10%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNV-YIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           L I ++  K    ++K++F   G + ++  IP        +G A+V    ++DA  A+QK
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP-------PRGCAYVCMETRQDAHRALQK 57

Query: 278 FNGQKFGKRPIAVDWAVPK 296
               K   + I V WA  K
Sbjct: 58  LRNVKLAGKKIKVAWAPNK 76

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 6/81 (7%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPV--GLVWNVYIPHNTDTG-LSKGFAFVKFTCKRDAESA 274
           +L +  IP      EI + FS V  G+V +V +  + D    ++GFAFV++   R A  A
Sbjct: 3   RLFVGGIPKTKTKEEILEEFSKVTEGVV-DVIVYRSPDDKNKNRGFAFVEYESHRAAAMA 61

Query: 275 IQKF-NGQ-KFGKRPIAVDWA 293
            +K   G+       +AVDWA
Sbjct: 62  RRKLVPGRILLWGHEVAVDWA 82

This subfamily corresponds to the RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. . Length = 82

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++ + N+P   +  +I+D+F   G +  + +  N   G    FAFV+F   RDAE A++ 
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL-KNRRRG--PPFAFVEFEDPRDAEDAVRG 57

Query: 278 FNGQKFGKRPIAVD 291
            +G  F    + V+
Sbjct: 58  RDGYDFDGYRLRVE 71

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 42.1 bits (100), Expect = 3e-05
 Identities = 17/58 (29%), Positives = 28/58 (48%)

Query: 429 FICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           F+  LP     E+V+  F  +G +     +  + T + KG  F+KF + E A  A+ A
Sbjct: 3   FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           IF+ NLPF +  +++K  F   G V+    V      R KG G + F++ E A  A+   
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVL-RADVKTDNDGRSKGFGTVLFESPEDAQRAIEMF 59

Query: 488 KTTSGLGIFLKGRQLTV 504
                 G  L+GR+L V
Sbjct: 60  N-----GYDLEGRELEV 71

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 16/36 (44%), Positives = 23/36 (63%)

Query: 8  NEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
             +G+G++QFA  EDA +A+E  NG  + GR I V
Sbjct: 37 GRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKV 72

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 42.1 bits (99), Expect = 3e-05
 Identities = 23/67 (34%), Positives = 40/67 (59%), Gaps = 1/67 (1%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           I + NLPF+   ++V+  FS++G++ S V V  +  +  +G  F++F T + A  A++A 
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKS-VRVPKKFDQSARGFAFVEFSTAKEALNAMNAL 61

Query: 488 KTTSGLG 494
           K T  LG
Sbjct: 62  KDTHLLG 68

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L + N+P      E K++FS  G V  V++         KGF F++   + +AE A  +
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFLN------KEKGFGFIRLDTRTNAEKAKAE 56

Query: 278 FNGQKFGKRPIAV 290
            +G     R + V
Sbjct: 57  LDGIMRKGRQLRV 69

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           I+I  LP++L   ++   FS +GE+V    V  + T + KG  FL ++   +   AV   
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 488 KTTSGLGIFLKGRQLTV 504
                 GI L GR + V
Sbjct: 72  N-----GIKLLGRTIRV 83

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 42.3 bits (99), Expect = 3e-05
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +  +P      E++ +FS  G +    I  +  TG+S+G  F++F  + +AE AI+  
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 279 NGQK--FGKRPIAVDWA 293
           NGQK      PI V +A
Sbjct: 64  NGQKPLGAAEPITVKFA 80

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 8/77 (10%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +RN+P      +++++FS  G V  V           K +AFV F  + DA  A+++ 
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKI--------KDYAFVHFEERDDAVKAMEEM 55

Query: 279 NGQKFGKRPIAVDWAVP 295
           NG++    PI V  A P
Sbjct: 56  NGKELEGSPIEVSLAKP 72

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 3/74 (4%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIP-HNTDTGLSKGFAFVKFTCKRDAESAIQKFN 279
           + N+P+     +IK+ F  + +  +V +P    D G  +GF + +F  +     A+   N
Sbjct: 6   LGNLPYDVTEEDIKEFFRGLNVS-SVRLPREPGDPGRLRGFGYAEFEDRDSLLQALS-LN 63

Query: 280 GQKFGKRPIAVDWA 293
            +    R I VD A
Sbjct: 64  DESLKNRRIRVDIA 77

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 7/78 (8%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +++ NL F++  ++++  F  FGE+          T R KG GF++F   E A  A+   
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKAL--- 57

Query: 488 KTTSGLGIF-LKGRQLTV 504
                L  F L GR + V
Sbjct: 58  ---EQLNGFELAGRPIKV 72

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 46.3 bits (110), Expect = 4e-05
 Identities = 29/99 (29%), Positives = 49/99 (49%), Gaps = 9/99 (9%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           IF+ NL   +DN+ +   FS FG ++S   V      + +G GF+ F+  E+A AA+   
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILS-CKVATDENGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 488 KTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETN 526
                 G+ L  +++ V + + K   H++E    K  TN
Sbjct: 150 N-----GMLLNDKEVYVGRFIKK---HEREAAPLKKFTN 180

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 11/75 (14%)

Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDA 271
            K +K K ++R I  K  V +I  ++ PV            +TG +KG+AFV+F    +A
Sbjct: 15  EKLEKLKKVLRKIFSKFGVGKIVGIYMPVD-----------ETGKTKGYAFVEFATPEEA 63

Query: 272 ESAIQKFNGQKFGKR 286
           + A++  NG K  K+
Sbjct: 64  KEAVKALNGYKLDKK 78

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 41.8 bits (98), Expect = 5e-05
 Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+P +   +E++ +F   G +    +  +  TGL +G AFV++  + +A++AI   
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 279 NGQKF--GKRPIAVDWA 293
           NG        P++V +A
Sbjct: 63  NGTIPPGSTMPLSVRYA 79

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 17/38 (44%), Positives = 20/38 (52%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVK 44
           N+ R F YVQF   E A  AV + NG    G K+ VK
Sbjct: 37 FNKTRRFCYVQFTSPESAAAAVALLNGKLGEGYKLVVK 74

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 3/60 (5%)

Query: 232 EIKDMFSPVGLVWNVYIPHNTD-TGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
            + D FS  G + +  +   TD  G SKG+ FV F  +  A  AI+K NG     + + V
Sbjct: 18  ALYDTFSAFGNILSCKV--ATDENGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKVFV 75

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 16/77 (20%)

Query: 580 LVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFV 639
           L + NLP   TE+ L++L           +   I+ ++ ++       D    S+G AFV
Sbjct: 1   LFVGNLPPDTTEEDLRELF---------SKFGEIESVRIVR-------DKDGKSKGFAFV 44

Query: 640 EFTEHQHALVALRVLNN 656
           EF   + A  AL  LN 
Sbjct: 45  EFESPEDAEKALEALNG 61

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 41.2 bits (97), Expect = 6e-05
 Identities = 15/39 (38%), Positives = 22/39 (56%)

Query: 3  TKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKI 41
          T   S   +GFGYV+F+  E A  A++   GT + GR +
Sbjct: 32 TDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDLLGRPV 70

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 45.3 bits (107), Expect = 6e-05
 Identities = 24/90 (26%), Positives = 35/90 (38%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
               S    + + + N+        +  +F P G V NV I  +  T   KG+ FV  T 
Sbjct: 261 QIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTN 320

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKN 297
             +A  AI   NG   G R + V +   K 
Sbjct: 321 YDEAAMAILSLNGYTLGNRVLQVSFKTNKA 350

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 41.6 bits (98), Expect = 6e-05
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 3/58 (5%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
            LI+  +P+K    ++KD FS  G +  V +  +  TG SKGF FV+F    D E  +
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFA---DYEDQV 55

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 41.6 bits (97), Expect = 6e-05
 Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++ +RN+PF     ++K+ FS  G V  ++     + G SKG   V+F     AE A + 
Sbjct: 1   QIFVRNLPFDLTWQKLKEKFSQCGHV--MFAEIKMENGKSKGCGTVRFDSPESAEKACRL 58

Query: 278 FNGQKFGKRPIAV 290
            NG K   R I V
Sbjct: 59  MNGIKINGREIDV 71

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 41.4 bits (98), Expect = 7e-05
 Identities = 18/70 (25%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           ++N+       ++K++F   G + +  +  + D G SKGF FV F     A+ A+++ NG
Sbjct: 6   VKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEELNG 64

Query: 281 QKFGKRPIAV 290
           ++   + + V
Sbjct: 65  KEVNGKKLYV 74

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 41.5 bits (98), Expect = 7e-05
 Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           +++ NL   +D+E +++ FS FG + S   V+     R KG GF+ F + E AT AV
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITS-AKVMTDEKGRSKGFGFVCFSSPEEATKAV 59

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 41.2 bits (97), Expect = 8e-05
 Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           + + +R  PF  K   I++ FSP+  V  + I  N   G   GFAFV    + D + A+ 
Sbjct: 1   FTVKMRGAPFNVKEKHIREFFSPLKPV-AIRIVKNDH-GRKTGFAFVDLKSEEDLKKAL- 57

Query: 277 KFNGQKFGKRPIAV 290
           K N    G R I +
Sbjct: 58  KRNKDYMGGRYIEL 71

This subfamily corresponds to the RRM2 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is also essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 41.0 bits (96), Expect = 8e-05
 Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 8/74 (10%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ + N+       E++ +F   G V +          + + FAFV    +  A+ AI++
Sbjct: 2   KIFVGNVDEDTSQEELRALFEAYGAVLSC--------AVMRQFAFVHLRGEAAADRAIEE 53

Query: 278 FNGQKFGKRPIAVD 291
            NG++   R + V+
Sbjct: 54  LNGRELHGRKLVVE 67

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 41.2 bits (96), Expect = 8e-05
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +  +P      E++ +FS  G +    I  +  TG+S+G  F++F  + +AE AI+  
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 279 NGQK--FGKRPIAVDWA 293
           NGQK      PI V +A
Sbjct: 65  NGQKPSGAAEPITVKFA 81

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 40.7 bits (96), Expect = 8e-05
 Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 7/63 (11%)

Query: 233 IKDMFSPVGLVWN--VYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
           + ++FS +G + +  +   H  D      +AFV++   R A +A+Q  NG+    + I V
Sbjct: 15  LAELFSQIGPIKSCKLIREHGNDP-----YAFVEYYDHRSAAAALQTMNGRLILGQEIKV 69

Query: 291 DWA 293
           +WA
Sbjct: 70  NWA 72

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 40.8 bits (96), Expect = 9e-05
 Identities = 27/78 (34%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            IF+ NLP D D   + Q FS FG V +   +    T + KG GF+     E A +A+++
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 487 SKTTSGLGIFLKGRQLTV 504
                  G  L GR L V
Sbjct: 63  LN-----GYRLGGRVLQV 75

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 44.9 bits (106), Expect = 9e-05
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +  +P     +E++ +FSP G +    I  +  TGLSKG  F++F  + +A+ AI+  
Sbjct: 92  LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151

Query: 279 NGQ--KFGKRPIAVDWA 293
           NG        PI V +A
Sbjct: 152 NGTTPSGCTEPITVKFA 168

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 41.3 bits (96), Expect = 9e-05
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +  +P      E++ +FS  G +    I  +  TG+S+G  F++F  + +AE AI+  
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 279 NGQK--FGKRPIAVDWA 293
           NGQK      PI V +A
Sbjct: 68  NGQKPPGATEPITVKFA 84

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 40.9 bits (96), Expect = 9e-05
 Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 8/73 (10%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L +R  P     + I+++FSP G V  V         +   FAFV+F     A  A   
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVK--------MISNFAFVEFESLESAIRAKDS 52

Query: 278 FNGQKFGKRPIAV 290
            +G+     P+ V
Sbjct: 53  VHGKVLNNNPLYV 65

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 40.9 bits (96), Expect = 9e-05
 Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 8/69 (11%)

Query: 225 PFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG 284
           P   +  +I+ +F P G +    I           FAFV+F    DA  A++  +G +  
Sbjct: 9   PGTTREEDIEKLFEPFGPLVRCDIRKT--------FAFVEFEDSEDATKALEALHGSRID 60

Query: 285 KRPIAVDWA 293
              + V++ 
Sbjct: 61  GSVLTVEFV 69

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 14/35 (40%), Positives = 21/35 (60%)

Query: 12 GFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          GFG+V +   EDA RA+   NG  +  ++I V +A
Sbjct: 43 GFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYA 77

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 40.9 bits (96), Expect = 1e-04
 Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 12/83 (14%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKR---PKGTGFLKFKTVEAAT 481
           ++ +F+  LPF +  EE+++ F   G V S    +  VT R   PKG  +++++   +A+
Sbjct: 2   KHKLFVSGLPFSVTKEELEKLFKKHGVVKS----VRLVTNRSGKPKGLAYVEYENESSAS 57

Query: 482 AAVSASKTTSGLGIFLKGRQLTV 504
            AV     T      +K + ++V
Sbjct: 58  QAVLKMDGTE-----IKEKTISV 75

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 5/78 (6%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ I+N+P      ++K              PH       + FAFV F  + + + A++ 
Sbjct: 7   KVEIKNLPKYIGFKQLKKFLKKQLF-----KPHKIKLLKRQDFAFVTFRSEEERQKALEI 61

Query: 278 FNGQKFGKRPIAVDWAVP 295
            +G K+  R ++   A P
Sbjct: 62  LDGFKWKGRVLSARLAKP 79

This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. . Length = 79

>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 254 TGLSKGFAFVKFTCKRDAESAIQKFNGQK-FGKRPIAVDWAVPK 296
            G S+G+ FV+F+ + + + A+ +  G    G +PI V  A+PK
Sbjct: 39  NGNSRGYGFVRFSDESEQKRALTEMQGASGLGGKPIRVSLAIPK 82

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 44.9 bits (106), Expect = 1e-04
 Identities = 21/76 (27%), Positives = 37/76 (48%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++ I N+P     ++IK++    G +    +  +  TGLSKG+AF ++      + AI  
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAA 356

Query: 278 FNGQKFGKRPIAVDWA 293
            NG+  G   + V  A
Sbjct: 357 LNGKDTGDNKLHVQRA 372

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 3/59 (5%)

Query: 230 VNE--IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN-GQKFGK 285
           V+E  +   F P G + ++ IP + +T   +GFAFV+F    DA +AI   N  + FG+
Sbjct: 10  VDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMNESELFGR 68

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 41.2 bits (96), Expect = 1e-04
 Identities = 25/79 (31%), Positives = 39/79 (49%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L I ++P +    ++  MF P G V +  +  +  T LSK F FV +     A++AIQ  
Sbjct: 10  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 279 NGQKFGKRPIAVDWAVPKN 297
           NG + G + + V     KN
Sbjct: 70  NGFQIGMKRLKVQLKRSKN 88

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           + N+ +K    ++K++F   G V    I  + + G S+G   V+F    +A  AI  FNG
Sbjct: 3   VANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMFNG 61

Query: 281 QKFGKRPIAV 290
           Q    RP+ V
Sbjct: 62  QMLFDRPMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 16/58 (27%), Positives = 32/58 (55%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           T+F+ N+P  + ++ +++     G+V+S+  V    T + K  GF +F+  E A  A+
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRAL 59

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 14/40 (35%), Positives = 25/40 (62%)

Query: 254 TGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA 293
           TG+S+G+ FV+F+ + D + A+ +  G   G RP+ +  A
Sbjct: 40  TGVSRGYGFVRFSDENDQQRALIEMQGVYCGGRPMRISTA 79

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 39.8 bits (94), Expect = 2e-04
 Identities = 14/38 (36%), Positives = 22/38 (57%)

Query: 4  KKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKI 41
           +  +  RGF +V+FA  EDA  A++  NG  + GR +
Sbjct: 31 VRNKDRPRGFAFVEFASPEDAEAALKKLNGLVLDGRTL 68

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 15/38 (39%), Positives = 21/38 (55%)

Query: 9  EHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
            RGF YVQF  + DA  A+   + T   GR+I ++ A
Sbjct: 40 RPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIEIQFA 77

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 9/80 (11%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPK---GTGFLKFKTVEAATAAV 484
           I++ NL F LD ++++  FS FGEV S      Q  K+ +   G  F+ FK   +A  A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 485 SASKTTSGLGIFLKGRQLTV 504
             + T       L GR+++V
Sbjct: 63  QLNGTE------LGGRKISV 76

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)

Query: 1  MVTKKGSNEH--RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          +  K G  +   RG+ +V F   E+A +A++  NG +  G+K+ V+ A
Sbjct: 32 LFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVVRWA 79

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 44.4 bits (105), Expect = 2e-04
 Identities = 24/95 (25%), Positives = 48/95 (50%), Gaps = 1/95 (1%)

Query: 190 ALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIP 249
            LL+ KE+  G    +         +   L ++N+      ++++++F+  G + +  + 
Sbjct: 152 MLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVM 211

Query: 250 HNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG 284
            +  +G S+GFAFV F    DA  A+++ NG+K G
Sbjct: 212 KD-GSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIG 245

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 44.5 bits (105), Expect = 2e-04
 Identities = 25/133 (18%), Positives = 54/133 (40%), Gaps = 8/133 (6%)

Query: 402 VSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQ 461
             + +  +S   + +     +    T+F+  L       ++ + FS  G+V     +  +
Sbjct: 66  SYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDR 125

Query: 462 VTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV-LKALDKKLAHDKEIDK 520
            ++R KG  +++F  VE+   A++ +      G  L GR + V     +K  A      +
Sbjct: 126 NSRRSKGVAYVEFYDVESVIKALALT------GQMLLGRPIIVQSSQAEKNRAAKAATHQ 179

Query: 521 SKNETNDHRNLYL 533
             +  N  + LY+
Sbjct: 180 PGDIPNFLK-LYV 191

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 39.8 bits (94), Expect = 2e-04
 Identities = 13/39 (33%), Positives = 21/39 (53%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKH 45
          +   +G+G+V F   E A RA+E  NG  +  +K+ V  
Sbjct: 39 NGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKVFVGP 77

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 17/73 (23%), Positives = 39/73 (53%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +  + +    ++++  F   G +  + +  +  TG  +G+AF++F  +RD ++A +  
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 279 NGQKFGKRPIAVD 291
           +G+K   R + VD
Sbjct: 64  DGKKIDGRRVLVD 76

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 218 KLIIRNIPFKAKVNEIKDMF-SPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           K+I+ N+P      +I++ F S +G +  V + +N + G S G A + F    DA  A  
Sbjct: 1   KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYN-EGGKSTGIANITFKRAGDATKAYD 59

Query: 277 KFNGQKF-GKRPIAVD 291
           KFNG+   G R + V+
Sbjct: 60  KFNGRIDDGNRKMKVE 75

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 254 TGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
           TG SKG+ FV+F  + + + A+ + NG     RP+ V
Sbjct: 40  TGRSKGYGFVRFGDEDERDRALTEMNGVYCSSRPMRV 76

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++I++N+P     + +++ F   G V +V +   T  G S+ F FV F  + DA+ A++ 
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKV-MRTRDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 278 FNGQKFGKRPIAVDWA 293
           FN        I+V+ A
Sbjct: 61  FNKTFIDTSKISVELA 76

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|241194 cd12750, RRM5_RBM12B, RNA recognition motif 5 in RNA-binding protein 12B (RBM12B) and similar proteins

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWN-VYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN 279
           + N+PFKA +NEI D F    ++ + V + +N + GL  G A V      +A +AI + N
Sbjct: 5   LENLPFKATINEILDFFHGYRVIPDSVSMQYN-EQGLPTGTAIVAMENYYEAMAAINELN 63

Query: 280 GQKFGKRPI 288
            +  G R +
Sbjct: 64  DRPIGPRKV 72

This subgroup corresponds to the RRM5 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear. . Length = 77

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 4/74 (5%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L ++N+P+   V+E+K++F       ++ +P     G SKG A+++F  + +AE A+++ 
Sbjct: 6   LFVKNLPYNITVDELKEVFEDAV---DIRLPSG-KDGSSKGIAYIEFKTEAEAEKALEEK 61

Query: 279 NGQKFGKRPIAVDW 292
            G +   R I VD+
Sbjct: 62  QGAEVDGRSIVVDY 75

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 16/82 (19%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQV----TKRPKGTGFLKFKTVEAATAA 483
           +++ NLPF + +EE+   F  +G +        Q+    TK  +GT F+ ++ +  A  A
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIR-------QIRIGNTKETRGTAFVVYEDIYDAKNA 57

Query: 484 VSASKTTSGLGIFLKGRQLTVL 505
                  SG  +    R L VL
Sbjct: 58  C---DHLSGFNV--ANRYLVVL 74

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 19/62 (30%), Positives = 29/62 (46%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           + I ++P      E+K  FS  G V NV +  +  TG SK + F++F     A  A +  
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 279 NG 280
           N 
Sbjct: 62  NN 63

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 24/72 (33%), Positives = 36/72 (50%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L I ++P +    E+  MF P G V +  +  +  T  SK F FV F     A++AIQ  
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 279 NGQKFGKRPIAV 290
           NG + G + + V
Sbjct: 67  NGFQIGMKRLKV 78

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 43.5 bits (102), Expect = 2e-04
 Identities = 23/87 (26%), Positives = 39/87 (44%)

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
              +      LI+  +P      E+  +F  +G +    I  +  TG S G+AFV F  +
Sbjct: 100 DNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSE 159

Query: 269 RDAESAIQKFNGQKFGKRPIAVDWAVP 295
            D++ AI+  NG     + + V +A P
Sbjct: 160 ADSQRAIKNLNGITVRNKRLKVSYARP 186

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 25/59 (42%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           KL I  +  K   N+I+ MFSP G +    I    D GLS+G AFV FT +  A++AI+
Sbjct: 3   KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIK 60

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 18/65 (27%), Positives = 37/65 (56%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++ +  IP     +E+  +F   G +W++ +  +  TGL++G+AFV F  K  A+ A++ 
Sbjct: 3   EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKL 62

Query: 278 FNGQK 282
           +N  +
Sbjct: 63  YNNHE 67

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 13/81 (16%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGT---GFLKFKTVEAATAA 483
           +IF+  L  D+  EE+ +RFS  G+++        + KR   T    F+KF+  +AA  A
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEV-----NLIKRANHTNAFAFIKFEREQAAARA 59

Query: 484 VSASKTTSGLGIFLKGRQLTV 504
           V +          LK + + V
Sbjct: 60  VESEN-----HSMLKNKTMHV 75

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSF-VPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           + I + N+PF+   +E+++ FS FGE+ +  +P     T   +G GF+ F T + A  A 
Sbjct: 1   SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAF 60

Query: 485 SASKTTSGLGIFLKGRQL 502
            A   ++     L GR+L
Sbjct: 61  KALCHST----HLYGRRL 74

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 19/73 (26%), Positives = 37/73 (50%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ I  +P     +++K++    G +    +  ++ TGLSKG+AF ++      + AI  
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 278 FNGQKFGKRPIAV 290
            NG + G + + V
Sbjct: 62  LNGMQLGDKKLTV 74

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 43.6 bits (103), Expect = 3e-04
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 228 AKVNEIK--DMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK 285
             V E K  D+F P G V +V +  ++ T  S G+ +V F    DAE A++  N ++ G 
Sbjct: 10  PDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGG 69

Query: 286 RPIAVDWAV 294
           +PI + W+ 
Sbjct: 70  KPIRIMWSQ 78

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 43.3 bits (102), Expect = 3e-04
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 5/64 (7%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
           M+ +KG +  RGFG+V F+  E+ANRAV   +G  +GG+ + V  A  +   EQRR+ + 
Sbjct: 318 MLDEKGVS--RGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRK---EQRRAHLQ 372

Query: 61  QEVQ 64
            +  
Sbjct: 373 DQFM 376

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 39.5 bits (92), Expect = 3e-04
 Identities = 20/59 (33%), Positives = 32/59 (54%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           +FI +LP +  + E+ Q F  FG V+S    + + T + K  GF+ F    +A AA+ A
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA 65

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 40.1 bits (93), Expect = 3e-04
 Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L I N+P      E+++M  P G V +  I  + + G+S+G  F +       E  IQ F
Sbjct: 4   LYISNLPVSMDEQELENMLKPFGHVISTRILRDAN-GVSRGVGFARMESTEKCEVVIQHF 62

Query: 279 NGQKFGKRP 287
           NG K+ K P
Sbjct: 63  NG-KYLKTP 70

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 19/59 (32%), Positives = 33/59 (55%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           +FI  L ++  ++ +K  FS +GE+   V +    TKR +G GF+ F +     AA++A
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
            T+F+  L      E +++ FS +G++     V   VT   KG  F++++    A  A  
Sbjct: 4   LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63

Query: 486 ASKTTSGLGIFLKGRQLTV 504
            +       + + G ++ V
Sbjct: 64  DAH-----KLVIDGSEIFV 77

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins

 Score = 39.5 bits (92), Expect = 3e-04
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L    + F     +++  F   G V +  + ++      K  AFVK   +RDAE+A +  
Sbjct: 6   LFPGGVTFNMIEYDLRSGFGRFGEVQSCILNND------KRHAFVKMYNRRDAENAREAM 59

Query: 279 NGQKFGKRPIAVDWAV 294
              K G   +   W V
Sbjct: 60  EQYKSGDMQLRTRWGV 75

This subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein encoded by gene NRD1 (for nuclear pre-mRNA down-regulation) from yeast S. cerevisiae. It is implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by polymerase II, and plays a critical role in pre-mRNA metabolism. Nrd1 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a short arginine-, serine-, and glutamate-rich segment similar to the regions rich in RE and RS dipeptides (RE/RS domains) in many metazoan splicing factors, and a proline- and glutamine-rich C-terminal domain (P+Q domain) similar to domains found in several yeast hnRNPs. Disruption of NRD1 gene is lethal to yeast cells. Its N-terminal domain is sufficient for viability, which may facilitate interactions with RNA polymerase II where Nrd1 may function as an auxiliary factor. By contrast, the RRM, RE/RS domains, and P+Q domain are dispensable. Seb1 is an RNA-binding protein encoded by gene seb1 (for seven binding) from fission yeast S. pombe. It is essential for cell viability and bound directly to Rpb7 subunit of RNA polymerase II. Seb1 is involved in processing of polymerase II transcripts. It also contains one RRM motif and a region rich in arginine-serine dipeptides (RS domain). Length = 79

>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 4/60 (6%)

Query: 232 EIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD 291
           ++ +  S  G V ++ +  N+     +G  +VKF     A+  IQ  NG+ F  R I  +
Sbjct: 27  DVLEECSKFGPVEHIKVDKNS----PEGVVYVKFKTVEAAQKCIQALNGRWFDGRQITAE 82

This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 39.4 bits (92), Expect = 3e-04
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+ F+   +E++  F  VG +  V +    D+G  KGFAFV F    + E A    
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDF---EEIEFATNAL 57

Query: 279 NGQKFGKRPIAVDWA 293
            G+    R + V++ 
Sbjct: 58  KGKHLNGRALRVEYG 72

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVW-NVYIPHNTDTGLSKGFAFVKFTCKRDAES 273
           +++R +P      +I++     G+   +V +     TG S+GFAFV+F    +A  
Sbjct: 5   IMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATR 60

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

>gnl|CDD|240948 cd12504, RRM2_hnRNPH_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWN-VYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN 279
           +R +PF     EI   FS + +V N + +P +   G S G A+V+F  +  AE A+ K +
Sbjct: 5   LRGLPFGCSKEEIAQFFSGLEIVPNGITLPMDYR-GRSTGEAYVQFASQESAERALGK-H 62

Query: 280 GQKFGKRPIAV 290
            +K G R I +
Sbjct: 63  KEKIGHRYIEI 73

This subfamily corresponds to the RRM2 of hnRNP H protein family which includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9). They represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing, having similar RNA binding affinities and specifically recognizing the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. Furthermore, hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in the splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. . Length = 77

>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           ++++N+P      E++++FS  G +  V +P     G++   A V+F    +A+ A +K 
Sbjct: 3   ILVKNLPAGTLTAELRELFSKFGSLGRVLLP---PAGIT---AIVEFLEPSEAKLAFRKL 56

Query: 279 NGQKFGKRPIAVDWA 293
              KF   P+ ++WA
Sbjct: 57  AYSKFKHVPLYLEWA 71

This subgroup corresponds to the RRM4 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 39.0 bits (91), Expect = 4e-04
 Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 5/78 (6%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T+F+ NL F +  E++   FS    +   V V    T   +G GF+ F  +E A  A++ 
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 487 SKTTSGLGIFLKGRQLTV 504
            K        L GR L +
Sbjct: 61  LKNKK-----LHGRILRL 73

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 38.3 bits (90), Expect = 4e-04
 Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 10/63 (15%)

Query: 442 VKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ 501
           + + FS FG V         + K+  G  F++F T EAA  AV         G+   GR 
Sbjct: 1   LYKLFSPFGNVEKIK-----LLKKKPGFAFVEFSTEEAAEKAVQYLN-----GVLFGGRP 50

Query: 502 LTV 504
           L V
Sbjct: 51  LRV 53

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L ++N+        +++ FSP G + +  +  + + G SKGF FV F+   +A  A+ +
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVTE 61

Query: 278 FNGQKFGKRPIAV 290
            NG+  G +P+ V
Sbjct: 62  MNGRIIGGKPLYV 74

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 15/35 (42%), Positives = 23/35 (65%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVK 44
          H+G+G+VQF   EDA  AV  +NG  + G+K+ + 
Sbjct: 34 HKGYGFVQFDNEEDARAAVAGENGREIAGQKLDIN 68

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 39.1 bits (91), Expect = 4e-04
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 3/62 (4%)

Query: 233 IKDMFSPVGLVWNVYI-PHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD 291
           +K +F   G V NV I P   + G++  + FV++    DAE A+Q  NG++     I V+
Sbjct: 15  LKQIFQVGGPVQNVKIIPDKNNKGVN--YGFVEYHQSHDAEIALQTLNGRQIENNEIRVN 72

Query: 292 WA 293
           WA
Sbjct: 73  WA 74

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 39.3 bits (91), Expect = 4e-04
 Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L I N+P      E+++M  P G V +  I  ++ +G S+G  F +       E+ I  F
Sbjct: 3   LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVISHF 61

Query: 279 NGQKFGKRPIAV 290
           NG KF K P  V
Sbjct: 62  NG-KFIKTPPGV 72

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 8/73 (10%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL + N+P      E++ +F   G V        T+  + K + FV    + DAE AI+ 
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTV--------TECDVVKNYGFVHMEEEEDAEDAIKA 52

Query: 278 FNGQKFGKRPIAV 290
            NG +F  + I V
Sbjct: 53  LNGYEFMGKRINV 65

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 39.1 bits (91), Expect = 4e-04
 Identities = 18/75 (24%), Positives = 37/75 (49%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+P    + E +++    G +   ++ ++  TG SKG+ FV++  K  A  A  + 
Sbjct: 2   LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLEL 61

Query: 279 NGQKFGKRPIAVDWA 293
            G++ G+  +   W 
Sbjct: 62  LGKQLGESTLFAQWM 76

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 8/75 (10%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           WK+ + N+      +E++ +F   G V         +    K +AFV    + +A +AI+
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEFGRV--------VECDKVKDYAFVHMEREEEALAAIE 52

Query: 277 KFNGQKFGKRPIAVD 291
             NG++   R I V+
Sbjct: 53  ALNGKEVKGRRINVE 67

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 17/59 (28%), Positives = 29/59 (49%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           TI + NL  D D +++++ F  FG +        + T + +G  F+ F T E A  A+ 
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE 59

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 8/81 (9%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQV---TKRPKGTGFLKFKTVEAATAA 483
            ++I NL   L    + + FS +G++  F  + H+      +P+G  F+ F+T E A  A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 484 VSASKTTSGLGIFLKGRQLTV 504
           + +       G    G++L V
Sbjct: 61  LKSLN-----GKTALGKKLVV 76

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 39.1 bits (92), Expect = 5e-04
 Identities = 19/45 (42%), Positives = 25/45 (55%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          V K    + +GFG+V F   E A +AVE  NG  V G+K+ V  A
Sbjct: 33 VMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEVNGKKLYVGRA 77

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 39.1 bits (92), Expect = 5e-04
 Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPK-----GTGFLKFKTVEAAT 481
           T+F+ NL F    E +K+ F   G V S      +  K P      G GF++FK+ EAA 
Sbjct: 2   TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 482 AAV 484
            A+
Sbjct: 62  KAL 64

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 7/65 (10%)

Query: 425 QNTIFICNLPFDLDNEE-VKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAA 483
             T+ + N+P +L+N   + + FS FG +V+      QV   P+    ++F T E A  A
Sbjct: 1   NTTLEVRNIPPELNNITKLNEHFSKFGTIVNI-----QVNYNPES-ALVQFSTSEEAKKA 54

Query: 484 VSASK 488
             + +
Sbjct: 55  YRSPE 59

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 38.6 bits (90), Expect = 5e-04
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++ + N+P   +  +++D+F   G + ++ + +         FAFV+F   RDAE A+  
Sbjct: 1   RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNR---RGLVPFAFVRFEDPRDAEDAVFG 57

Query: 278 FNGQKFGKRPIAVDW 292
            NG  FG+  + V++
Sbjct: 58  RNGYDFGQCRLRVEF 72

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 38.8 bits (91), Expect = 6e-04
 Identities = 16/57 (28%), Positives = 29/57 (50%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAA 483
            + + NLP +  +E+ ++  S FG V     V  + T   KG GF+++ +  +A  A
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA 57

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 38.6 bits (90), Expect = 6e-04
 Identities = 16/38 (42%), Positives = 24/38 (63%)

Query: 6  GSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
           + +H+GF +V++ V E A  A+E  NG  +GGR I V
Sbjct: 37 VTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKV 74

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 38.4 bits (90), Expect = 6e-04
 Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           + N+ +    +E++ +FS  G + +V +      G SKG+A+V+F  +   + A+ K + 
Sbjct: 4   VSNLDYSVPEDELRKLFSKCGEITDVRLV-KNYKGKSKGYAYVEFENEESVQEAL-KLDR 61

Query: 281 QKFGKRPIAVD 291
           +    RP+ V 
Sbjct: 62  ELIKGRPMFVS 72

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 38.4 bits (90), Expect = 6e-04
 Identities = 13/61 (21%), Positives = 30/61 (49%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T+F+  L   +   ++ + FS  G+V     +  + ++R KG  +++F   E+   A+  
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

Query: 487 S 487
           +
Sbjct: 61  T 61

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 42.6 bits (100), Expect = 6e-04
 Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 230 VNEIKDMFSPVGLVWNVYIPH---NTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKR 286
             ++K  FS  G + N+ IP    + ++    G  F+++   R AE A++  NG+KF  R
Sbjct: 433 YEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDR 492

Query: 287 PI 288
            +
Sbjct: 493 VV 494

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 38.4 bits (90), Expect = 6e-04
 Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 9/59 (15%)

Query: 428 IFICNLPFD-LDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           +F+ NL  D +  E++++ FS +G+++     LH      KG GF++F   E A AAV+
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGIS--LH------KGYGFVQFDNEEDARAAVA 53

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 38.7 bits (91), Expect = 6e-04
 Identities = 12/53 (22%), Positives = 25/53 (47%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
           +F+  L   +   ++++RFS FG V     +  +     +G  ++  +T EA 
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQ 54

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 38.5 bits (90), Expect = 6e-04
 Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAAT 481
           D  Q  +F+ NLP D+  +E+K+ F  FG V+           R    GF+ F   EA  
Sbjct: 2   DSHQ--LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQ 59

Query: 482 AAVSASKTTS 491
             ++      
Sbjct: 60  KILANKPIYF 69

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 38.5 bits (90), Expect = 6e-04
 Identities = 18/73 (24%), Positives = 31/73 (42%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +  +    K  ++K +FS  G V    I  N  +  ++ F FV      +A   IQ  
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 279 NGQKFGKRPIAVD 291
           +  +   R I+V+
Sbjct: 62  HRTELHGRVISVE 74

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 38.3 bits (90), Expect = 7e-04
 Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 9/75 (12%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           + + NLP D+   ++    S FG+V + + +L       K    ++  +VE+A + V   
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNVL-LLRG-----KNQALVEMDSVESAKSMVDYY 55

Query: 488 KTTSGLGIFLKGRQL 502
            T   L   ++GR++
Sbjct: 56  LTVPAL---IRGRRV 67

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 38.3 bits (89), Expect = 7e-04
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 8/70 (11%)

Query: 225 PFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG 284
           P   +  +++  F P G + NV I  N        FAFV++  + DA  A++  N  K  
Sbjct: 9   PINTRTRDLERHFEPYGKLVNVRIRRN--------FAFVQYETQEDATKALESTNMSKVL 60

Query: 285 KRPIAVDWAV 294
            R I+V++A 
Sbjct: 61  DRVISVEYAA 70

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 38.4 bits (90), Expect = 8e-04
 Identities = 18/39 (46%), Positives = 26/39 (66%), Gaps = 1/39 (2%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
          +GFG+V+FA  E A +A+E K+G  + GR+I V  A  R
Sbjct: 40 KGFGHVEFATEEGAQKALE-KSGEELLGREIRVDLATER 77

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 38.4 bits (89), Expect = 8e-04
 Identities = 18/56 (32%), Positives = 35/56 (62%), Gaps = 1/56 (1%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKF-KTVEAATA 482
           +++  LP  +  +E++Q FS +G +++   ++ QVT   +G GF++F K +EA  A
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEA 59

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 42.2 bits (99), Expect = 8e-04
 Identities = 24/95 (25%), Positives = 43/95 (45%), Gaps = 6/95 (6%)

Query: 413 KSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFL 472
           K +  T   D  ++ I+I NLP  L  +++K+   +FG++ +F  +    T   KG  F 
Sbjct: 284 KLVNSTTVLDS-KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFC 342

Query: 473 KFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
           ++K       A++A       G      +L V +A
Sbjct: 343 EYKDPSVTDVAIAALN-----GKDTGDNKLHVQRA 372

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|240936 cd12492, RRM2_RBM46, RNA recognition motif 2 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 38.4 bits (89), Expect = 8e-04
 Identities = 28/82 (34%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPV--GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           +L I +IP + K  EI +    V  G++  +  P  TD   ++GFAFV++   R A  A 
Sbjct: 4   RLFIGSIPKEKKKEEILEEMKKVTEGVMDVIVYPSATDRTKNRGFAFVEYESHRAAAMAR 63

Query: 276 QKFNGQKFG--KRPIAVDWAVP 295
           +K     F      I VDWA P
Sbjct: 64  RKLIPGTFQLWGHTIQVDWACP 85

This subgroup corresponds to the RRM2 of RBM46, also termed cancer/testis antigen 68 (CT68). It is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 85

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 38.2 bits (89), Expect = 8e-04
 Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 7/78 (8%)

Query: 428 IFICNLPFDLDNEEVKQRF-SAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           +FI N+P+DL  +++K  F    GEV ++V +      + +G G ++FK  E+   A+  
Sbjct: 2   VFISNIPYDLKWQDLKDLFREKVGEV-TYVELFKDEEGKSRGCGVVEFKDKESVQKALET 60

Query: 487 SKTTSGLGIFLKGRQLTV 504
                     LKGR+L V
Sbjct: 61  MNRYE-----LKGRKLVV 73

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 38.5 bits (89), Expect = 9e-04
 Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           ++I NLP  +D +E++     FG+V+S   +L   +   +G GF + ++ E   A +S
Sbjct: 3   LYISNLPLSMDEQELENMLKPFGQVIS-TRILRDSSGTSRGVGFARMESTEKCEAVIS 59

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 38.5 bits (90), Expect = 9e-04
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL +  IP   +  +++ +F   G ++ + +  +  TG+ KG AF+ +  +  A  A   
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66

Query: 278 FNGQKF---GKRPIAV 290
            + QK      RPI V
Sbjct: 67  LHEQKTLPGMNRPIQV 82

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 38.7 bits (89), Expect = 9e-04
 Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 420 GEDELQNT-IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVE 478
           G D+L  T ++I  LP +  ++++ +    +G++VS   +L + T + KG GF+ F +  
Sbjct: 1   GWDQLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPA 60

Query: 479 AATAAVSASKTT 490
           AA  AVSA K +
Sbjct: 61  AAQKAVSALKAS 72

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 13/39 (33%), Positives = 23/39 (58%)

Query: 5  KGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
          + + E RGF +V+F    DA  A++  +G  + GR++ V
Sbjct: 34 RYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRELRV 72

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +F+ NLP+    +++++ FS FGE+      + + + + KG  ++ F   E A  A    
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 488 KTTSGLGIFLKGRQLTVLKA 507
                  +F +GR + +L  
Sbjct: 65  DGK----VF-QGRLIHILPG 79

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 18/43 (41%), Positives = 25/43 (58%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
          +V  + +   RGFG+V F  +EDA  A E  NG  + GR+I V
Sbjct: 31 VVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRV 73

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 12/82 (14%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSF-VPVLHQVTKRPKGTGF--LKFKTVEAATA 482
           +T+++ N P   D  +++  F  +GE++S   P L     R     F  ++F + E+A A
Sbjct: 1   STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRR----FCYVQFTSPESAAA 56

Query: 483 AVSASKTTSGLGIFLKGRQLTV 504
           AV+      G     +G +L V
Sbjct: 57  AVALLNGKLG-----EGYKLVV 73

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 37.8 bits (87), Expect = 0.001
 Identities = 18/56 (32%), Positives = 35/56 (62%), Gaps = 1/56 (1%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKF-KTVEAATA 482
           +++  LP  +  +E++Q FS +G +++   ++ QVT   +G GF++F K +EA  A
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 60

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 14/57 (24%), Positives = 30/57 (52%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           +++  L  ++D + +   F  FG++      L   T++ +G  F++F+  E A AA+
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 41.2 bits (96), Expect = 0.001
 Identities = 28/112 (25%), Positives = 54/112 (48%), Gaps = 13/112 (11%)

Query: 379 ALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQT---EGEDELQNT-IFICNLP 434
           A V    E DS + +           LN    + K LK +    G + +++T +++ NLP
Sbjct: 152 AFVDFGSEADSQRAIK---------NLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLP 202

Query: 435 FDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
             + ++++   F  +G++V    +  ++T  P+G  F++F   E A  A+SA
Sbjct: 203 RTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISA 254

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 5/83 (6%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G EG       L I ++P +    ++   F P G V +  +  +  T LSK F FV +  
Sbjct: 1   GPEGCN-----LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDN 55

Query: 268 KRDAESAIQKFNGQKFGKRPIAV 290
              A++AIQ  NG + G + + V
Sbjct: 56  PDSAQAAIQAMNGFQIGTKRLKV 78

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 38.5 bits (89), Expect = 0.001
 Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L I N+P      E++ M  P G V +  I  +  +G S+G  F +       E+ I  F
Sbjct: 3   LYISNLPLSMDEQELESMLKPFGQVISTRILRDA-SGTSRGVGFARMESTEKCEAIITHF 61

Query: 279 NGQKFGKRPIAV 290
           NG K+ K P  V
Sbjct: 62  NG-KYIKTPPGV 72

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 3/56 (5%)

Query: 237 FSPVGLVWNVYIPHNTDTGLSKGF-AFVKFTCKRDAESAIQKFNGQK-FGKRPIAV 290
           FS  GL+++V +        + GF AFVKF   R A  A +  NG+  F   P+ V
Sbjct: 25  FSQFGLLYSVKV-FPNAAVATPGFYAFVKFYSARAASRAQKACNGKWLFQGSPLKV 79

This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA. . Length = 81

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 38.0 bits (88), Expect = 0.001
 Identities = 21/52 (40%), Positives = 30/52 (57%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
           +FI  L +D   +++K  FS FGEVV     L  +T R +G GF+ FK  E+
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESES 52

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 18/72 (25%), Positives = 27/72 (37%), Gaps = 6/72 (8%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           + NIP      ++  +F   G +       +      +GFAFVK      A  AI +  G
Sbjct: 5   VGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQLQG 58

Query: 281 QKFGKRPIAVDW 292
                RP+   W
Sbjct: 59  FPVHGRPLRCGW 70

This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 8/76 (10%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++ I  +P++A+  +++  F   G +  +         L  GF FV+F   RDA+ A+ +
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREIN--------LKNGFGFVEFEDPRDADDAVYE 52

Query: 278 FNGQKFGKRPIAVDWA 293
            NG++     + V+ A
Sbjct: 53  LNGKELCGERVIVEHA 68

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240950 cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein hnRNP H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 26/68 (38%), Positives = 40/68 (58%), Gaps = 3/68 (4%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           +R +P++A  N+I + FSP+  V NV I +N D G + G A V+F    DA +A+ K + 
Sbjct: 5   MRGLPYRATENDIFEFFSPLNPV-NVRIEYNAD-GRATGEADVEFATHEDAVAAMSK-DR 61

Query: 281 QKFGKRPI 288
           +  G R I
Sbjct: 62  EHMGHRYI 69

This subfamily corresponds to the RRM3 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in the splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. For instance, members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. The family also includes a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 also contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity. . Length = 75

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 37.9 bits (88), Expect = 0.001
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 1/79 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++ +  I FK   N+++  FS  G V  V I ++   G+SKG+ FV F  + DA+  +Q+
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQE 62

Query: 278 FNGQKFGKRPIAVDWAVPK 296
            N   F  + + +  A+ K
Sbjct: 63  ANRLCFRDKKLNIGQAIRK 81

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 232 EIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           +++ +F P G +    I    D G SKG AFVKF+   +A++AI   +G
Sbjct: 17  DVRRLFEPFGTIEECTILRGPD-GNSKGCAFVKFSSHAEAQAAINALHG 64

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L I N+P      +++ M  P G V +  I  ++  G S+G  F +   +   E  I KF
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSK-GQSRGVGFARMESREKCEDIISKF 61

Query: 279 NG 280
           NG
Sbjct: 62  NG 63

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding protein RBM12, RBM12B and similar proteins

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWN-VYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN 279
           I+NIPF     E+   F+ + +    ++I ++  TG + G A+V+F  + DA  A  + +
Sbjct: 4   IKNIPFDVTKGEVLAFFAGIAIAEQGIHILYD-KTGKTLGEAYVEFVSEEDAMRAE-RLH 61

Query: 280 GQKFGKRPIAV 290
            +K   R I +
Sbjct: 62  RKKLKGREILL 72

This subfamily corresponds to the RRM4 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. . Length = 73

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 4  KKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
          +K    + GF +V F     A  A+++ NGT +GGRKI V
Sbjct: 38 EKQGRLNNGFAFVTFKDASSAENALQL-NGTELGGRKISV 76

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 16/56 (28%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKF-KTVEAATA 482
           +++  LP  +  +E++  FS +G +++   +   VT   +G GF++F K +EA  A
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERA 58

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 41.0 bits (96), Expect = 0.002
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 1/68 (1%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
            +  KA+  ++ + FS VG V +V    + ++  SKG A+V+F        A+    GQ 
Sbjct: 96  QLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQM 154

Query: 283 FGKRPIAV 290
              RPI V
Sbjct: 155 LLGRPIIV 162

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 16/60 (26%), Positives = 28/60 (46%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            ++I +LP      E+++ FS FG V        + T + KG  F++F++ E A      
Sbjct: 1   VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAET 60

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 427 TIFICN-LPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           T  I N LP ++  +E++  FS+ GE+ S   +  +VT +  G GF+ +   E A  A++
Sbjct: 2   TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 13/44 (29%), Positives = 26/44 (59%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVK 44
          +   +  N  RG+ YV+F   EDA +A++  +G  + G+++ V+
Sbjct: 30 LPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTVE 73

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           T+++ NLP  L  EE+++ FS FG       +      + KG  F++F T EAA  A+
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFG------AIEEVRVFKDKGYAFVRFDTHEAAATAI 53

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 37.7 bits (88), Expect = 0.002
 Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 2/40 (5%)

Query: 7  SNEHRGFG--YVQFAVMEDANRAVEMKNGTSVGGRKIGVK 44
          S   R  G  Y +F+  E A + V+  NG     RK+ VK
Sbjct: 40 SRRVRPLGIAYAEFSSPEQAEKVVKDLNGKVFKNRKLFVK 79

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 12/84 (14%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQV------TKRPKGTGFLKFKTVEAA 480
            ++I NL +    E++++    F  V   +P    V        RP G  + +F + E A
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPS-QTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 481 TAAVSASKTTSGLGIFLKGRQLTV 504
              V         G   K R+L V
Sbjct: 60  EKVVKDLN-----GKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 37.5 bits (86), Expect = 0.002
 Identities = 18/56 (32%), Positives = 35/56 (62%), Gaps = 1/56 (1%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKF-KTVEAATA 482
           +++  LP  +  +E++Q FS +G +++   ++ QVT   +G GF++F K +EA  A
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 63

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           I + NLP  +  + +++ F + GEV   V V+     + +  GF+ FK+ E A  AV 
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTD-VKVMRTRDGKSRRFGFVGFKSEEDAQQAVK 59

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +RN+PFK    E+ D+F   G +  + I +  +T   +G AFV +    DA++A    
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACDHL 61

Query: 279 NGQKFGKRPIAV 290
           +G     R + V
Sbjct: 62  SGFNVANRYLVV 73

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 3/80 (3%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            I+I +LP     +E+K+ FS FG V +      + T   K  GF++F   E A     A
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAI---A 57

Query: 487 SKTTSGLGIFLKGRQLTVLK 506
           +K+ +   +  K  Q+ VL 
Sbjct: 58  AKSMNNYLLMGKVLQVHVLP 77

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 17/76 (22%), Positives = 38/76 (50%), Gaps = 13/76 (17%)

Query: 218 KLIIRNIP-FKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLS--KGFAFVKFTCKRDAESA 274
           ++ + N+   K    +++++FS  G +           G+S  KG+ FV+F  + DA +A
Sbjct: 2   RVFVGNLNTDKVSKEDLEEIFSKYGKI----------LGISLHKGYGFVQFDNEEDARAA 51

Query: 275 IQKFNGQKFGKRPIAV 290
           +   NG++   + + +
Sbjct: 52  VAGENGREIAGQKLDI 67

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 5/67 (7%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTD-----TGLSKGFAFVKFTCKRDAES 273
           L ++N+ FK     +K  F   G V +V I    D       LS G+ FV+F  K  A+ 
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 274 AIQKFNG 280
           A+++  G
Sbjct: 63  ALKRLQG 69

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMF-SPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           ++ I NIP+  K  ++KD+F   VG V  V +    + G S+G   V+F  K   + A++
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVEL-FKDEEGKSRGCGVVEFKDKESVQKALE 59

Query: 277 KFNGQKFGKRPIAV 290
             N  +   R + V
Sbjct: 60  TMNRYELKGRKLVV 73

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           ++I NLP  +D +E++     FG+V+S   +L   +   +G GF + ++ E   A ++
Sbjct: 3   LYISNLPLSMDEQELESMLKPFGQVIS-TRILRDASGTSRGVGFARMESTEKCEAIIT 59

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 6/68 (8%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGT--GFLKFKTVEAATAAV 484
           TI +  +   L  +++K+ FS  GEV      +     R       F++F   E+A +A+
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVTR----VRLCGDRQHSARFAFVEFADAESALSAL 57

Query: 485 SASKTTSG 492
           + S T  G
Sbjct: 58  NLSGTLLG 65

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 18/48 (37%), Positives = 30/48 (62%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFK 475
           +F+  L ++   E +++ FS +GEVV  V +  + T R +G GF+KFK
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFK 49

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 41.2 bits (96), Expect = 0.002
 Identities = 40/150 (26%), Positives = 66/150 (44%), Gaps = 20/150 (13%)

Query: 155 LPKEELEQHGLAQEGCK--MDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGS 212
           LPK   EQ    Q+  K  M+ S      +K         HQ++        +Q      
Sbjct: 52  LPKLSSEQKDDIQKAKKYAMEQS------IKQVLLKQTKAHQQQQLENQQRQQQ------ 99

Query: 213 KTQKWKLIIR----NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
           + Q   ++ R    +I F+ + + I+  F P G + ++ +  +  TG  KGFAFV++   
Sbjct: 100 RQQALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVP 159

Query: 269 RDAESAIQKFNGQKFGKRPIAVDWAVPKNI 298
             A+ A+++ NGQ  G R I V    P N+
Sbjct: 160 EAAQLALEQMNGQMLGGRNIKVG--RPSNM 187

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

>gnl|CDD|240934 cd12490, RRM2_ACF, RNA recognition motif 2 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 29/83 (34%), Positives = 40/83 (48%), Gaps = 6/83 (7%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPV--GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           +L +  IP   K  EI      V  G++  +  P   D   ++GFAFV++   R A  A 
Sbjct: 4   RLFVGGIPKTKKREEILAEMKKVTDGVLDVIVYPSAADKAKNRGFAFVEYESHRAAAMAR 63

Query: 276 QKF---NGQKFGKRPIAVDWAVP 295
           +K      Q +G  PIAVDWA P
Sbjct: 64  RKLLPGRIQLWG-HPIAVDWAEP 85

This subgroup corresponds to the RRM2 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 85

>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 19/59 (32%), Positives = 33/59 (55%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           +FI  L F+  +E ++  F  +G +   V +    TKR +G GF+ + +VE   AA++A
Sbjct: 5   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 7/76 (9%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKF-KTVEAATAAVSA 486
           IF+ +L  ++D E ++  F+ FGE+     V    T + KG GF+ F K  +A  A  S 
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 487 SKTTSGLGIFLKGRQL 502
           +      G +L GR +
Sbjct: 62  N------GQWLGGRAI 71

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 427 TIFICN-LPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           T  I N LP D+  EE++  F A G + S   V  ++T +  G GF+ +     A  A++
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 486 A 486
            
Sbjct: 61  T 61

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 27/94 (28%), Positives = 39/94 (41%), Gaps = 24/94 (25%)

Query: 581 VIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHY-------S 633
           V+  LP    EK L+KL            K V+++I        GK+   +        +
Sbjct: 5   VVDGLPVVGEEK-LEKL------------KKVLRKI--FSKFGVGKIVGIYMPVDETGKT 49

Query: 634 RGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCF 667
           +G AFVEF   + A  A++ LN    KL   H F
Sbjct: 50  KGYAFVEFATPEEAKEAVKALNG--YKLDKKHTF 81

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 15/58 (25%), Positives = 30/58 (51%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           +F+ NL F+   +E++  F   G +     +  + + + KG  F+ F+ +E AT A+ 
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALK 58

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           + + N+ +K    ++K++FS  G+V    I  + D G S+G   V F    +A  AI  F
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKD-GKSRGIGTVTFEQPIEAVQAISMF 61

Query: 279 NGQKFGKRPIAV 290
           NGQ    RP+ V
Sbjct: 62  NGQLLFDRPMHV 73

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           + + N+ FK    ++K++FS  G V    I  + D G S+G   V F    +A  AI  F
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKD-GKSRGMGTVTFEQPIEAVQAISMF 61

Query: 279 NGQKFGKRPIAV 290
           NGQ    RP+ V
Sbjct: 62  NGQFLFDRPMHV 73

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 10/68 (14%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLS---KGFAFVKFTCKRDAESAIQKFN 279
           N+P   +  E++D+F   G + ++      D  L     G+AF++F   RDAE AI+  +
Sbjct: 6   NLPGDIREREVEDLFYKYGPIVDI------DLKLPPRPPGYAFIEFEDARDAEDAIRGRD 59

Query: 280 GQKF-GKR 286
           G  F G+R
Sbjct: 60  GYDFDGQR 67

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 13/58 (22%), Positives = 34/58 (58%), Gaps = 2/58 (3%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVS-FVPVLHQVTKRPKGTGFLKFKTVEAATAA 483
           ++++ N+      +++++ F  +G +V  ++P+    T+RP+G  +++F+ V  A  A
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFY-TRRPRGFAYVQFEDVRDAEDA 58

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 13/38 (34%), Positives = 24/38 (63%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVK 44
          +  H+G+G+V+F   EDA+ A+++ N   + G+ I V 
Sbjct: 36 TQAHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPIRVN 73

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 12/50 (24%), Positives = 27/50 (54%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFK 475
            T+F+  L +D    ++++ F  +G +     V  + T +P+G  F++F+
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFE 51

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 232 EIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
           E+ + FS  G +  V +    +   +  FAF+KF  ++ A  A++  N      + + V
Sbjct: 19  ELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAVESENHSMLKNKTMHV 75

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 4/60 (6%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L + N+P     +E+K+ F   G V  V I      G    F FV F    D   A+QK
Sbjct: 5   QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVF----DDPEAVQK 60

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 3/60 (5%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T+++ NLP D+   EV+  F  +G +V    +  ++  RP G  F++F+    A  A+  
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVD---IDLKLPPRPPGYAFIEFEDARDAEDAIRG 57

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 36.6 bits (84), Expect = 0.004
 Identities = 19/59 (32%), Positives = 33/59 (55%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           +FI  L F+  ++ +++ F  +G +   V +    TKR +G GF+ +  VE   AA+SA
Sbjct: 5   LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 7/71 (9%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L++ N+      ++I ++FS +G +    +       +  G A V +  K DA +AI K
Sbjct: 2   RLVVSNLHPSVTEDDIVELFSAIGALKRARL-------VRPGVAEVVYVRKDDALTAIDK 54

Query: 278 FNGQKFGKRPI 288
           +N ++   +P+
Sbjct: 55  YNNRELDGQPM 65

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 36.4 bits (84), Expect = 0.004
 Identities = 19/52 (36%), Positives = 30/52 (57%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
           +F+  L +D   +++K+ FS FGEVV     +  VT R +G GF+ FK   +
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAAS 52

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 10/79 (12%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T+++  L   +  ++++  F  FGE+ S + V+ +     +   F+ F T EAA  A  A
Sbjct: 3   TLYVGGLGERVTEKDLRDHFYQFGEIRS-ITVVPR-----QQCAFVTFTTREAAEKA--A 54

Query: 487 SKTTSGLGIFLKGRQLTVL 505
            +  + L   + GR+L + 
Sbjct: 55  ERLFNKL--IINGRRLKLK 71

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 6/75 (8%)

Query: 223 NIPFKAKVNEI---KDM---FSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           N+ F  K+N +   +D+   FS  G + +  +  +  TG S  +AF++F  K D E A  
Sbjct: 4   NVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYF 63

Query: 277 KFNGQKFGKRPIAVD 291
           K +      R I VD
Sbjct: 64  KMDNVLIDDRRIHVD 78

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 10/61 (16%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTG---FLKFKTVEAATA 482
           NT+F+ NL  +   EE++Q FS         P   ++    KG G   F++F+ V  AT 
Sbjct: 3   NTLFVANLGPNTTEEELRQLFSRQ-------PGFRRLKMHNKGGGPVCFVEFEDVSFATQ 55

Query: 483 A 483
           A
Sbjct: 56  A 56

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

>gnl|CDD|241190 cd12746, RRM2_RBM12B, RNA recognition motif 2 in RNA-binding protein 12B (RBM12B) and similar proteins

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 9/70 (12%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWN--VYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           L +R +PF    + ++D FS  GL  +  +++ +    GL+ G + VKF  K DA   ++
Sbjct: 2   LFLRGLPFSVTEDNVRDFFS--GLKVDGVIFLKNRR--GLNNGNSMVKFATKEDAIEGLK 57

Query: 277 K---FNGQKF 283
           +   + G ++
Sbjct: 58  RDRQYMGSRY 67

This subgroup corresponds to the RRM2 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear. . Length = 78

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	676
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	100.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	100.0
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	100.0
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.97
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.97
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.96
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.95
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.95
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.94
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.93
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.93
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.92
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.92
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.91
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.9
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.89
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.88
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.88
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.86
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.85
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.85
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.84
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.76
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.75
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.74
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.74
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.71
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.7
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.7
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.67
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.65
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.63
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.63
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.61
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.61
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.6
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.58
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.57
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.53
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.52
KOG0122	270	consensus Translation initiation factor 3, subunit	99.51
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.5
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.49
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.48
KOG0122	270	consensus Translation initiation factor 3, subunit	99.48
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.47
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.46
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.45
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.41
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.41
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.39
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.39
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.37
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.37
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.36
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.35
PLN03120	260	nucleic acid binding protein; Provisional	99.35
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.34
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.34
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.34
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.32
PLN03120	260	nucleic acid binding protein; Provisional	99.31
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.3
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.3
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.3
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.29
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.28
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.28
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.28
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.26
PLN03213	759	repressor of silencing 3; Provisional	99.25
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.24
smart00362	72	RRM_2 RNA recognition motif.	99.24
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.24
PLN03121	243	nucleic acid binding protein; Provisional	99.24
PLN03213	759	repressor of silencing 3; Provisional	99.23
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.23
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.23
smart00360	71	RRM RNA recognition motif.	99.21
PLN03121	243	nucleic acid binding protein; Provisional	99.2
smart00362	72	RRM_2 RNA recognition motif.	99.2
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.18
smart00360	71	RRM RNA recognition motif.	99.16
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.15
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.15
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.12
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.12
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.11
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.08
smart00361	70	RRM_1 RNA recognition motif.	99.08
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.07
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.06
smart00361	70	RRM_1 RNA recognition motif.	99.01
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.01
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.0
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.97
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.96
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.86
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.83
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.8
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.79
KOG4210	285	consensus Nuclear localization sequence binding pr	98.79
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.77
KOG0226	290	consensus RNA-binding proteins [General function p	98.73
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.7
KOG4210	285	consensus Nuclear localization sequence binding pr	98.69
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.66
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.6
KOG0226	290	consensus RNA-binding proteins [General function p	98.59
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.57
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.56
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.55
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.54
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.48
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.42
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.36
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.35
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.22
KOG0151	877	consensus Predicted splicing regulator, contains R	98.21
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.21
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.2
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.16
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.1
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.07
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.03
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.02
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.98
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.95
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.87
KOG0151	877	consensus Predicted splicing regulator, contains R	97.87
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.85
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.4
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.34
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.29
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.2
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.05
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.95
KOG2314	698	consensus Translation initiation factor 3, subunit	96.94
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.89
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.84
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.81
KOG3152	278	consensus TBP-binding protein, activator of basal	96.77
KOG2314	698	consensus Translation initiation factor 3, subunit	96.68
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.57
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.51
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.44
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.35
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.33
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.25
KOG3152	278	consensus TBP-binding protein, activator of basal	96.12
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.0
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.82
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.7
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.66
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.47
KOG1855	484	consensus Predicted RNA-binding protein [General f	95.46
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.36
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.33
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	95.2
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.7
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	94.63
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.48
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	94.27
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.27
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.44
KOG2068	327	consensus MOT2 transcription factor [Transcription	93.18
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	92.64
KOG2591	684	consensus c-Mpl binding protein, contains La domai	92.3
KOG2068	327	consensus MOT2 transcription factor [Transcription	91.98
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	91.71
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	90.38
KOG2591	684	consensus c-Mpl binding protein, contains La domai	90.21
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	89.55
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	89.52
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	89.39
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	88.93
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	88.7
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	88.52
KOG2135	526	consensus Proteins containing the RNA recognition	88.42
KOG2135	526	consensus Proteins containing the RNA recognition	88.13
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	86.45
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	84.49
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	83.5
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	82.94
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	81.67
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	80.35

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=1.9e-60  Score=480.82  Aligned_cols=493  Identities=38%  Similarity=0.548  Sum_probs=373.5

Q ss_pred             CcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCe
Q 005812          121 ARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGG  200 (676)
Q Consensus       121 ~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~  200 (676)
                      +.||||++||++++.++|.++|+.+|+|..+.+..++.         .+.++|||||.|.-.++++.|++..++..|.|+
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~g---------s~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr   75 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKG---------SSEKRGFGFVTFAMEEDVQRALAETEQSKFEGR   75 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCC---------cccccCccceeeehHhHHHHHHHHhhcCcccce
Confidence            36999999999999999999999999999999887653         257899999999999999999999999999999


Q ss_pred             EEEEecCCCC------------------------CC--CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCC
Q 005812          201 TVWARQLGGE------------------------GS--KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDT  254 (676)
Q Consensus       201 ~i~v~~~~~~------------------------~~--~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~  254 (676)
                      .|.+......                        ..  ..+.+.|+|+|||+.+...+|+.+|+.||.|..|.||+.. .
T Consensus        76 ~l~v~~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-d  154 (678)
T KOG0127|consen   76 ILNVDPAKKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-D  154 (678)
T ss_pred             ecccccccccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-C
Confidence            9987432100                        01  1237899999999999999999999999999999999876 4


Q ss_pred             CCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCC--CCCCCCCCCC-Ccccc
Q 005812          255 GLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNS--DSGSDDDLGD-DDAET  331 (676)
Q Consensus       255 ~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~-~~~~~  331 (676)
                      |+-+|||||+|....+|..||+.+|+..|.||+|.|+||.+++.|.......+..-......  +...++++.. .+...
T Consensus       155 gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed  234 (678)
T KOG0127|consen  155 GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEED  234 (678)
T ss_pred             CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhc
Confidence            55559999999999999999999999999999999999999998887554321110000000  0000000000 00000


Q ss_pred             cCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCC
Q 005812          332 ASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSK  411 (676)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  411 (676)
                      .+.++++++..++    ++....                           .+........+.+..+ .++..  .+....
T Consensus       235 ~e~d~edeEe~D~----~se~~e---------------------------e~~~~Eee~~~vDd~e-~S~~~--~~~k~~  280 (678)
T KOG0127|consen  235 GEEDSEDEEETDG----NSEAFE---------------------------EGEESEEEEDDVDDEE-SSGKK--ESDKKA  280 (678)
T ss_pred             ccccccccccccc----cchhhh---------------------------cccccccccccccccc-ccccC--cccchh
Confidence            0001111110010    000000                           0000000000000000 00000  000000


Q ss_pred             CCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCC
Q 005812          412 PKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTS  491 (676)
Q Consensus       412 ~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~  491 (676)
                      ..+.  ...+...+.+|||+||||++|+++|.++|++||.|.++.|+.++.++.++|.|||.|.+..+|+.||.......
T Consensus       281 q~k~--~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~  358 (678)
T KOG0127|consen  281 QNKT--TRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPAS  358 (678)
T ss_pred             cccc--ccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccC
Confidence            0000  12355667999999999999999999999999999999999999999999999999999999999999986555


Q ss_pred             CCC-eeecCcEEEEEEccCchhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCC
Q 005812          492 GLG-IFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQS  570 (676)
Q Consensus       492 ~~g-~~l~gr~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  570 (676)
                      +.| +.|+||.|.|..|..+.++..+++++......+++||||..+|.|..++|++.++|..||..|....+.+.+++.+
T Consensus       359 e~g~~ll~GR~Lkv~~Av~RkeA~dmeqkk~~Kk~~gkrNLyLa~EG~I~~gt~aAeglS~~Dm~kRer~~~~k~k~lkn  438 (678)
T KOG0127|consen  359 EDGSVLLDGRLLKVTLAVTRKEAADMEQKKKRKKPKGKRNLYLAREGLIRDGTPAAEGLSATDMAKRERIAERKRKKLKN  438 (678)
T ss_pred             CCceEEEeccEEeeeeccchHHHHHHHHHhhhhccCCccceeeeccCccccCChhhcccchhhHHHHHHHHHHHHHhhcC
Confidence            445 9999999999999999999999888877888899999999999999999999999999999999999999999999


Q ss_pred             CCccccCCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHH
Q 005812          571 PNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVA  650 (676)
Q Consensus       571 p~~~~~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~A  650 (676)
                      ||+++|.|+|.|+|||..++...|..|..++|++.+.+.-..+..+..+....      .+.+.||+||.|..+++|.+|
T Consensus       439 pnlhlSrtRL~i~Nlpramn~KqL~~Ll~~Av~~~at~~kk~~R~~~~le~~~------k~~s~g~aF~~f~EhEhalka  512 (678)
T KOG0127|consen  439 PNLHLSRTRLVIRNLPRAMNPKQLNRLLRDAVTGFATKVKKCIRQIKFLEEEK------KNYSEGYAFVGFTEHEHALKA  512 (678)
T ss_pred             CceeeehhhhhhhcCccccCHHHHHHHHHHHHhhhhhhcchhhhhhhhHHhhh------hcccccccccCccHHHHHHHh
Confidence            99999999999999999999999999999999998775333333333322211      357899999999999999999


Q ss_pred             HHHHcCCCCCCCcccCcccccc
Q 005812          651 LRVLNNNPSKLFYHHCFDAADA  672 (676)
Q Consensus       651 i~~lng~~~~~~~~~~~~~~~~  672 (676)
                      ++.+       |+.+|++|.-+
T Consensus       513 lk~~-------G~lkq~~Vefe  527 (678)
T KOG0127|consen  513 LKVL-------GVLKQAKVEFE  527 (678)
T ss_pred             hhcc-------cccccceEEEE
Confidence            9987       77888888654

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=100.00  E-value=4.8e-50  Score=450.67  Aligned_cols=357  Identities=21%  Similarity=0.272  Sum_probs=297.2

Q ss_pred             EEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeEE
Q 005812          123 TVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTV  202 (676)
Q Consensus       123 ~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~i  202 (676)
                      +|||+|||.++++++|+++|+.||.|.+|+++.++.         .++++|||||+|.+.++|++|+..+|+..+.|+.|
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~---------t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i   72 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSV---------TRRSLGYGYVNFQNPADAERALETMNFKRLGGKPI   72 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC---------CCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeE
Confidence            699999999999999999999999999999998764         37899999999999999999999999999999999


Q ss_pred             EEecCCCC--CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCC
Q 005812          203 WARQLGGE--GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG  280 (676)
Q Consensus       203 ~v~~~~~~--~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~  280 (676)
                      ++......  .......+|||+|||.++++++|+++|+.||.|.+|+++.+. +|+++|||||+|.+.++|.+|++.|||
T Consensus        73 ~i~~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~lng  151 (562)
T TIGR01628        73 RIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNG  151 (562)
T ss_pred             EeecccccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHhcc
Confidence            98654321  223345689999999999999999999999999999999874 788999999999999999999999999


Q ss_pred             ceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHH
Q 005812          281 QKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKV  360 (676)
Q Consensus       281 ~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  360 (676)
                      ..+.|+.|.|....++.....                                                           
T Consensus       152 ~~~~~~~i~v~~~~~~~~~~~-----------------------------------------------------------  172 (562)
T TIGR01628       152 MLLNDKEVYVGRFIKKHEREA-----------------------------------------------------------  172 (562)
T ss_pred             cEecCceEEEecccccccccc-----------------------------------------------------------
Confidence            999999999987644321000                                                           


Q ss_pred             hhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHH
Q 005812          361 LNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNE  440 (676)
Q Consensus       361 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~tee  440 (676)
                                                                                 ......++|||+|||+++|++
T Consensus       173 -----------------------------------------------------------~~~~~~~~l~V~nl~~~~tee  193 (562)
T TIGR01628       173 -----------------------------------------------------------APLKKFTNLYVKNLDPSVNED  193 (562)
T ss_pred             -----------------------------------------------------------ccccCCCeEEEeCCCCcCCHH
Confidence                                                                       000113689999999999999


Q ss_pred             HHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec----CcEEEEEEccCchhhhhH
Q 005812          441 EVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK----GRQLTVLKALDKKLAHDK  516 (676)
Q Consensus       441 dl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~----gr~l~v~~a~~k~~~~~~  516 (676)
                      +|+++|+.||.|.++.++.+. ++.++|||||+|.+.++|.+|++.|+     +..|.    |+.|.|.++..+......
T Consensus       194 ~L~~~F~~fG~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~-----g~~i~~~~~g~~l~v~~a~~k~er~~~  267 (562)
T TIGR01628       194 KLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMN-----GKKIGLAKEGKKLYVGRAQKRAEREAE  267 (562)
T ss_pred             HHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhC-----CcEecccccceeeEeecccChhhhHHH
Confidence            999999999999999988874 68899999999999999999999999     99999    999999998876543211


Q ss_pred             hhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCeEEEecCCcccCHHHHHH
Q 005812          517 EIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKK  596 (676)
Q Consensus       517 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~V~nlp~~~te~~l~~  596 (676)
                      ...+..                                       .......    .....++|||+|||..+|+++|++
T Consensus       268 ~~~~~~---------------------------------------~~~~~~~----~~~~~~~l~V~nl~~~~~~~~L~~  304 (562)
T TIGR01628       268 LRRKFE---------------------------------------ELQQERK----MKAQGVNLYVKNLDDTVTDEKLRE  304 (562)
T ss_pred             HHhhHH---------------------------------------hhhhhhh----cccCCCEEEEeCCCCccCHHHHHH
Confidence            111000                                       0000000    011336799999999999999999


Q ss_pred             HHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCCCCCcccCccccccccc
Q 005812          597 LCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAADAQCK  675 (676)
Q Consensus       597 ~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~~~~~~~~~~~~~~~~~  675 (676)
                      +|+         .||.|.+|+++.+. +      +.++|+|||+|.+.++|.+|+..|||..   ...+.+.|.+|+.|
T Consensus       305 ~F~---------~~G~i~~~~i~~d~-~------g~~~g~gfV~f~~~~~A~~A~~~~~g~~---~~gk~l~V~~a~~k  364 (562)
T TIGR01628       305 LFS---------ECGEITSAKVMLDE-K------GVSRGFGFVCFSNPEEANRAVTEMHGRM---LGGKPLYVALAQRK  364 (562)
T ss_pred             HHH---------hcCCeEEEEEEECC-C------CCcCCeEEEEeCCHHHHHHHHHHhcCCe---eCCceeEEEeccCc
Confidence            999         59999999999983 3      5899999999999999999999999942   23477888888765

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=100.00  E-value=1.7e-47  Score=429.92  Aligned_cols=328  Identities=22%  Similarity=0.340  Sum_probs=274.6

Q ss_pred             CcccCCCCcccceEEEEecCHHHHHHHHHHhCCceecCeEEEEeeccccchHHHhhhhhchhhhhhhhhhccCCCCCccc
Q 005812            1 MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAEDIEKTMDNKDGVIS   80 (676)
Q Consensus         1 ~v~~~~tg~s~G~afV~F~~~edA~~Al~~~~g~~i~gr~i~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (676)
                      |++|+.|++++|||||+|.+.+||++||+.+|+..|.|++|+|.|+......                            
T Consensus        32 v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~~----------------------------   83 (562)
T TIGR01628        32 VCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPSL----------------------------   83 (562)
T ss_pred             EEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccccc----------------------------
Confidence            4688999999999999999999999999999999999999999998322100                            


Q ss_pred             ccccccchhhccCCCCCCCcccccCcccCCCCccchhcccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhh
Q 005812           81 GAEKHSSKLLESGKTVKPRKAATLGIDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEEL  160 (676)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~  160 (676)
                                                          ......+|||+|||.++++++|+++|+.||.|.+|+++.+    
T Consensus        84 ------------------------------------~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~----  123 (562)
T TIGR01628        84 ------------------------------------RRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD----  123 (562)
T ss_pred             ------------------------------------cccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeec----
Confidence                                                0012346999999999999999999999999999998865    


Q ss_pred             hhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeEEEEecCCCC-----CCCCCCcEEEEcCCCCCCCHHHHHH
Q 005812          161 EQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGE-----GSKTQKWKLIIRNIPFKAKVNEIKD  235 (676)
Q Consensus       161 ~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~i~v~~~~~~-----~~~~~~~~v~V~nLp~~~~e~~l~~  235 (676)
                            ..|+++|||||+|.+.++|.+|+..+||..+.|+.+.+......     ......++|||+|||.++++++|++
T Consensus       124 ------~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~  197 (562)
T TIGR01628       124 ------ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRE  197 (562)
T ss_pred             ------CCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccccccccccccCCCeEEEeCCCCcCCHHHHHH
Confidence                  34889999999999999999999999999999999988543221     1234457899999999999999999


Q ss_pred             hhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC----CeeEEEEEecCCCCCCcCCcccCccCC
Q 005812          236 MFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG----KRPIAVDWAVPKNIYSSGGAAAGVQNK  311 (676)
Q Consensus       236 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~----g~~i~v~~a~~~~~~~~~~~~~~~~~~  311 (676)
                      +|+.||.|.++.++.+. +|.++|||||+|.+.++|.+|++.|+|..+.    |+.+.|.++..+.....          
T Consensus       198 ~F~~fG~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~----------  266 (562)
T TIGR01628       198 LFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREA----------  266 (562)
T ss_pred             HHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhHH----------
Confidence            99999999999999885 7889999999999999999999999999999    99999988755431100          


Q ss_pred             CCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCch
Q 005812          312 GDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDK  391 (676)
Q Consensus       312 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~  391 (676)
                                                                  ..........                          
T Consensus       267 --------------------------------------------~~~~~~~~~~--------------------------  276 (562)
T TIGR01628       267 --------------------------------------------ELRRKFEELQ--------------------------  276 (562)
T ss_pred             --------------------------------------------HHHhhHHhhh--------------------------
Confidence                                                        0000000000                          


Q ss_pred             hhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEE
Q 005812          392 TVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGF  471 (676)
Q Consensus       392 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~af  471 (676)
                                               ........+.+|||+|||..+++++|+++|+.||.|.+|+++.+ .++.++||||
T Consensus       277 -------------------------~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gf  330 (562)
T TIGR01628       277 -------------------------QERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGF  330 (562)
T ss_pred             -------------------------hhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEE
Confidence                                     00001123478999999999999999999999999999999998 6799999999


Q ss_pred             EEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhh
Q 005812          472 LKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAH  514 (676)
Q Consensus       472 V~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~  514 (676)
                      |+|.+.++|.+|+..||     |..|+|++|.|.+|..+....
T Consensus       331 V~f~~~~~A~~A~~~~~-----g~~~~gk~l~V~~a~~k~~~~  368 (562)
T TIGR01628       331 VCFSNPEEANRAVTEMH-----GRMLGGKPLYVALAQRKEQRR  368 (562)
T ss_pred             EEeCCHHHHHHHHHHhc-----CCeeCCceeEEEeccCcHHHH
Confidence            99999999999999999     999999999999999887543

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=100.00  E-value=4.7e-46  Score=407.37  Aligned_cols=433  Identities=17%  Similarity=0.208  Sum_probs=277.4

Q ss_pred             CcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHh--CCCeec
Q 005812          121 ARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALL--HQKEIK  198 (676)
Q Consensus       121 ~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l--~~~~~~  198 (676)
                      +++|||+|||+++++++|+++|+.||.|.+|.++.               +++||||+|.+.++|.+|+..+  ++..+.
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~---------------~k~~afVef~~~e~A~~Ai~~~~~~~~~l~   66 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP---------------GKRQALVEFEDEESAKACVNFATSVPIYIR   66 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC---------------CCCEEEEEeCchHHHHHHHHHhhcCCceEc
Confidence            57899999999999999999999999999999763               3579999999999999999974  789999


Q ss_pred             CeEEEEecCCCCC------------CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEec
Q 005812          199 GGTVWARQLGGEG------------SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFT  266 (676)
Q Consensus       199 ~~~i~v~~~~~~~------------~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~  266 (676)
                      |+.|+|.......            .......|||+||++.+++++|+++|+.||.|.+|.|+++.    .+++|||+|.
T Consensus        67 g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~----~~~~afVef~  142 (481)
T TIGR01649        67 GQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN----NVFQALVEFE  142 (481)
T ss_pred             CeEEEEEecCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC----CceEEEEEEC
Confidence            9999986432111            11122479999999999999999999999999999998753    3478999999


Q ss_pred             CHHHHHHHHHHhCCceeCC--eeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCC
Q 005812          267 CKRDAESAIQKFNGQKFGK--RPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDL  344 (676)
Q Consensus       267 ~~~~A~~A~~~l~~~~~~g--~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (676)
                      +.++|.+|++.|||..|.|  +.|+|+|+++..+.........      .+.+        ..+..+..+.. ..     
T Consensus       143 ~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s------~dyt--------~~~l~~~~~~~-~~-----  202 (481)
T TIGR01649       143 SVNSAQHAKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDS------RDYT--------NPDLPGRRDPG-LD-----  202 (481)
T ss_pred             CHHHHHHHHHHhcCCcccCCceEEEEEEecCCCceeEecccCC------CCCc--------CCCCCCCCCCC-cC-----
Confidence            9999999999999999954  6899999987665432211000      0000        00000000000 00     


Q ss_pred             CCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCC---C-----chhhccccccccccccCCCCCCC-CCC
Q 005812          345 PSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQD---S-----DKTVNESAKVSDVSKLNSSKSKP-KSL  415 (676)
Q Consensus       345 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~---~-----~~~~~~~~~~~~~~~~~~~~~~~-~~~  415 (676)
                         ..+..       ....   ..+..+.    .....|+....   .     ..............+.......+ ...
T Consensus       203 ---~~~~~-------~~~~---~~~~~~~----~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (481)
T TIGR01649       203 ---QTHRQ-------RQPA---LLGQHPS----SYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAIS  265 (481)
T ss_pred             ---ccccc-------cccc---cccCCCc----cCCCcccccCCCCCCcccccccCCCcccCCCCCcccccccccCcccc
Confidence               00000       0000   0000000    00000000000   0     00000000000000000000000 000


Q ss_pred             CcccCCCCCCCeEEEcCCCC-CCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCC
Q 005812          416 KQTEGEDELQNTIFICNLPF-DLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLG  494 (676)
Q Consensus       416 ~~~~~~~~~~~~l~V~nLp~-~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g  494 (676)
                      ........++++|||+|||+ .+|+++|+++|+.||.|.+|+|++++     +|||||+|.+.++|..|+..||     |
T Consensus       266 ~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~ln-----g  335 (481)
T TIGR01649       266 SYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLN-----G  335 (481)
T ss_pred             ccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhC-----C
Confidence            00111245678999999998 69999999999999999999998763     6999999999999999999999     9


Q ss_pred             eeecCcEEEEEEccCchhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCcc
Q 005812          495 IFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFH  574 (676)
Q Consensus       495 ~~l~gr~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~  574 (676)
                      ..|.|++|.|.++.........                   ++....+.+...+.+.....+.   .  ........+..
T Consensus       336 ~~l~g~~l~v~~s~~~~~~~~~-------------------~~~~~~~~~~~~d~~~~~~~r~---~--~~~~~~~~~~~  391 (481)
T TIGR01649       336 VKLFGKPLRVCPSKQQNVQPPR-------------------EGQLDDGLTSYKDYSSSRNHRF---K--KPGSANKNNIQ  391 (481)
T ss_pred             CEECCceEEEEEcccccccCCC-------------------CCcCcCCCcccccccCCccccC---C--CcccccccccC
Confidence            9999999999997654211100                   0000000000000000000000   0  00000000112


Q ss_pred             ccCCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCC--ceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHH
Q 005812          575 VSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPV--IKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALR  652 (676)
Q Consensus       575 ~~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~--V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~  652 (676)
                      .+..+|||.|||..+|+++|+++|+         .||.  |..|++....        +..+|+|||+|.+.++|.+||.
T Consensus       392 ~ps~~L~v~NLp~~~tee~L~~lF~---------~~G~~~i~~ik~~~~~--------~~~~~~gfVeF~~~e~A~~Al~  454 (481)
T TIGR01649       392 PPSATLHLSNIPLSVSEEDLKELFA---------ENGVHKVKKFKFFPKD--------NERSKMGLLEWESVEDAVEALI  454 (481)
T ss_pred             CCCcEEEEecCCCCCCHHHHHHHHH---------hcCCccceEEEEecCC--------CCcceeEEEEcCCHHHHHHHHH
Confidence            2457899999999999999999999         4897  8888886432        1357999999999999999999


Q ss_pred             HHcCCCCC
Q 005812          653 VLNNNPSK  660 (676)
Q Consensus       653 ~lng~~~~  660 (676)
                      .|||+++-
T Consensus       455 ~ln~~~l~  462 (481)
T TIGR01649       455 ALNHHQLN  462 (481)
T ss_pred             HhcCCccC
Confidence            99998664

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=6.3e-43  Score=371.56  Aligned_cols=343  Identities=22%  Similarity=0.277  Sum_probs=237.0

Q ss_pred             cEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeE
Q 005812          122 RTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGT  201 (676)
Q Consensus       122 ~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~  201 (676)
                      .+|||+|||.++++++|+++|+.||+|.+|+|+.++.         +|+++|||||+|.+.++|.+|+..|||..|.|+.
T Consensus         4 ~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~---------~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~   74 (352)
T TIGR01661         4 TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKV---------TGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKT   74 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCC---------CCccceEEEEEECcHHHHHHHHhhcccEEECCee
Confidence            5799999999999999999999999999999998874         4899999999999999999999999999999999


Q ss_pred             EEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCc
Q 005812          202 VWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQ  281 (676)
Q Consensus       202 i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~  281 (676)
                      |.|............++|||+|||..+++++|+.+|+.||.|..+.++.+..++.++|||||+|.+.++|+.|++.|||.
T Consensus        75 i~v~~a~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~  154 (352)
T TIGR01661        75 IKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGT  154 (352)
T ss_pred             EEEEeecccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCC
Confidence            99976554444556789999999999999999999999999999999998888889999999999999999999999999


Q ss_pred             eeCC--eeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHH
Q 005812          282 KFGK--RPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARK  359 (676)
Q Consensus       282 ~~~g--~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  359 (676)
                      .+.|  ..|.|.|+.............................-....  .+........... .+....+  .......
T Consensus       155 ~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~-~~~~~~~--~~~~~~~  229 (352)
T TIGR01661       155 TPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTA--AGIGPMHHAAARF-RPSAGDF--TAVLAHQ  229 (352)
T ss_pred             ccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccc--cCCCCccCccccc-ccCcchh--hhhhhhh
Confidence            9876  678888886543211110000000000000000000000000  0000000000000 0000000  0000000


Q ss_pred             HhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCC-CCCCC-cccCCCCCCCeEEEcCCCCCC
Q 005812          360 VLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSK-PKSLK-QTEGEDELQNTIFICNLPFDL  437 (676)
Q Consensus       360 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~-~~~~~~~~~~~l~V~nLp~~~  437 (676)
                      ....      ..+....                      .....+....... ..... ........+.+|||+|||+++
T Consensus       230 ~~~~------~~~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~  281 (352)
T TIGR01661       230 QQQH------AVAQQHA----------------------AQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDT  281 (352)
T ss_pred             hhhc------ccccccc----------------------cccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCC
Confidence            0000      0000000                      0000000000000 00000 001123446789999999999


Q ss_pred             CHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCch
Q 005812          438 DNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       438 teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~  511 (676)
                      ++++|+++|++||.|.+|+|+.|..++.++|||||+|.+.++|.+|+..||     |..|+||.|.|.|+.+|.
T Consensus       282 ~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~ln-----G~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       282 DETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLN-----GYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             CHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhC-----CCEECCeEEEEEEccCCC
Confidence            999999999999999999999999899999999999999999999999999     999999999999988764

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=3.6e-42  Score=365.76  Aligned_cols=316  Identities=22%  Similarity=0.322  Sum_probs=232.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      +..+|||+|||..+++++|+++|+.||.|.+|+|++++.+|+++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            35799999999999999999999999999999999999899999999999999999999999999999999999999986


Q ss_pred             CCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCC
Q 005812          295 PKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSL  374 (676)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  374 (676)
                      +...                                                                            
T Consensus        82 ~~~~----------------------------------------------------------------------------   85 (352)
T TIGR01661        82 PSSD----------------------------------------------------------------------------   85 (352)
T ss_pred             cccc----------------------------------------------------------------------------
Confidence            5421                                                                            


Q ss_pred             CCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE
Q 005812          375 SDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS  454 (676)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~  454 (676)
                                                                     ...+++|||+|||..+++++|+++|+.||.|..
T Consensus        86 -----------------------------------------------~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~  118 (352)
T TIGR01661        86 -----------------------------------------------SIKGANLYVSGLPKTMTQHELESIFSPFGQIIT  118 (352)
T ss_pred             -----------------------------------------------ccccceEEECCccccCCHHHHHHHHhccCCEEE
Confidence                                                           001368999999999999999999999999999


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC--cEEEEEEccCchhhhhHhhhh--hcccccccCc
Q 005812          455 FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG--RQLTVLKALDKKLAHDKEIDK--SKNETNDHRN  530 (676)
Q Consensus       455 v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g--r~l~v~~a~~k~~~~~~~~~~--~~~~~~~~~~  530 (676)
                      +.++.+..++.++|||||+|.+.++|.+|++.||     |..+.|  ++|.|.++..+..........  ..........
T Consensus       119 ~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~-----g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~  193 (352)
T TIGR01661       119 SRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLN-----GTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTR  193 (352)
T ss_pred             EEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhC-----CCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCC
Confidence            9999988888999999999999999999999999     888877  578899887654222111110  0000000000


Q ss_pred             cccc---ccCcccCCCCCCCCCCh--hHHHHHHHHHHHHh------------------------hcCCCCCccccCCeEE
Q 005812          531 LYLA---KEGLILEGTPAAEGVSD--DDMSKRQMLHEKKM------------------------TKLQSPNFHVSRTRLV  581 (676)
Q Consensus       531 ~~~~---~~g~~~~~~~~~~~~~~--~~~~~~~~~~~~~~------------------------~~~~~p~~~~~~~~l~  581 (676)
                      ..+.   ..+...+.........+  ..............                        .....+.....+.+||
T Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lf  273 (352)
T TIGR01661       194 VPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIF  273 (352)
T ss_pred             CCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCccccccccccccCCCCCCCCCCCcEEE
Confidence            0000   00000000000001110  00000000000000                        0000011111234699


Q ss_pred             EecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCCCC
Q 005812          582 IYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKL  661 (676)
Q Consensus       582 V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~~~  661 (676)
                      |+|||+.+++++|+++|+         +||.|.+|+|++|+.++      .++|||||+|.+.++|.+||..|||..+  
T Consensus       274 V~NL~~~~~e~~L~~~F~---------~fG~v~~v~i~~d~~t~------~skG~aFV~F~~~~~A~~Ai~~lnG~~~--  336 (352)
T TIGR01661       274 VYNLSPDTDETVLWQLFG---------PFGAVQNVKIIRDLTTN------QCKGYGFVSMTNYDEAAMAILSLNGYTL--  336 (352)
T ss_pred             EeCCCCCCCHHHHHHHHH---------hCCCeEEEEEeEcCCCC------CccceEEEEECCHHHHHHHHHHhCCCEE--
Confidence            999999999999999999         69999999999998765      8999999999999999999999999643  


Q ss_pred             CcccCcccccccccC
Q 005812          662 FYHHCFDAADAQCKT  676 (676)
Q Consensus       662 ~~~~~~~~~~~~~~~  676 (676)
                       ..+++.|+++-.|+
T Consensus       337 -~gr~i~V~~~~~~~  350 (352)
T TIGR01661       337 -GNRVLQVSFKTNKA  350 (352)
T ss_pred             -CCeEEEEEEccCCC
Confidence             34788888877663

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=100.00  E-value=1.9e-39  Score=355.35  Aligned_cols=337  Identities=19%  Similarity=0.211  Sum_probs=244.1

Q ss_pred             cccceEEEEecCHHHHHHHHHH--hCCceecCeEEEEeeccccchHHHhhhhhchhhhhhhhhhccCCCCCccccccccc
Q 005812            9 EHRGFGYVQFAVMEDANRAVEM--KNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAEDIEKTMDNKDGVISGAEKHS   86 (676)
Q Consensus         9 ~s~G~afV~F~~~edA~~Al~~--~~g~~i~gr~i~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (676)
                      ++||||||+|.+.++|++|++.  +++..|.|++|+|.++.++...  +. .  +                         
T Consensus        36 ~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~~--~~-~--~-------------------------   85 (481)
T TIGR01649        36 PGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIK--RD-G--N-------------------------   85 (481)
T ss_pred             CCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcccc--cC-C--C-------------------------
Confidence            3679999999999999999997  4789999999999999544100  00 0  0                         


Q ss_pred             chhhccCCCCCCCcccccCcccCCCCccchhcccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccc
Q 005812           87 SKLLESGKTVKPRKAATLGIDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLA  166 (676)
Q Consensus        87 ~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~  166 (676)
                                         .+ .+..    ......+|||+||++++++++|+++|+.||.|.+|.++.++         
T Consensus        86 -------------------~~-~~~~----~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~---------  132 (481)
T TIGR01649        86 -------------------SD-FDSA----GPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN---------  132 (481)
T ss_pred             -------------------Cc-ccCC----CCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC---------
Confidence                               00 0000    00123479999999999999999999999999999976432         


Q ss_pred             cCCCccceEEEEeCCHHHHHHHHHHhCCCeecCe--EEEEecCC----------------------C-------------
Q 005812          167 QEGCKMDASAVLYTTVKSACASVALLHQKEIKGG--TVWARQLG----------------------G-------------  209 (676)
Q Consensus       167 ~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~--~i~v~~~~----------------------~-------------  209 (676)
                          ..++|||+|.+.++|.+|+..|||..|.+.  .|.+....                      +             
T Consensus       133 ----~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~  208 (481)
T TIGR01649       133 ----NVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQR  208 (481)
T ss_pred             ----CceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCcccccc
Confidence                246899999999999999999999999754  33321000                      0             


Q ss_pred             -C-----------------------------------------------------------CCCCCCcEEEEcCCCC-CC
Q 005812          210 -E-----------------------------------------------------------GSKTQKWKLIIRNIPF-KA  228 (676)
Q Consensus       210 -~-----------------------------------------------------------~~~~~~~~v~V~nLp~-~~  228 (676)
                       .                                                           ......++|||+|||+ .+
T Consensus       209 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~v  288 (481)
T TIGR01649       209 QPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKV  288 (481)
T ss_pred             ccccccCCCccCCCcccccCCCCCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCC
Confidence             0                                                           0012457999999998 69


Q ss_pred             CHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCc
Q 005812          229 KVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGV  308 (676)
Q Consensus       229 ~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~  308 (676)
                      ++++|+++|+.||.|.+|+|+++     .+|||||+|.+.++|..|+..|||..|.|+.|+|.++...........    
T Consensus       289 t~~~L~~lF~~yG~V~~vki~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~----  359 (481)
T TIGR01649       289 NCDRLFNLFCVYGNVERVKFMKN-----KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREG----  359 (481)
T ss_pred             CHHHHHHHHHhcCCeEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCC----
Confidence            99999999999999999999986     469999999999999999999999999999999999865432111000    


Q ss_pred             cCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCC
Q 005812          309 QNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQD  388 (676)
Q Consensus       309 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~  388 (676)
                           . ..      +   .               ......+..                                    
T Consensus       360 -----~-~~------~---~---------------~~~~~d~~~------------------------------------  373 (481)
T TIGR01649       360 -----Q-LD------D---G---------------LTSYKDYSS------------------------------------  373 (481)
T ss_pred             -----c-Cc------C---C---------------CcccccccC------------------------------------
Confidence                 0 00      0   0               000000000                                    


Q ss_pred             CchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCc--eeEEEEeecCCCCCc
Q 005812          389 SDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGE--VVSFVPVLHQVTKRP  466 (676)
Q Consensus       389 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~--v~~v~i~~~~~~~~~  466 (676)
                                     ....+... +..........++.+|||+|||+.+++++|+++|+.||.  |..++++... ++ .
T Consensus       374 ---------------~~~~r~~~-~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~-~~-~  435 (481)
T TIGR01649       374 ---------------SRNHRFKK-PGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKD-NE-R  435 (481)
T ss_pred             ---------------CccccCCC-cccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCC-CC-c
Confidence                           00000000 000000012235689999999999999999999999998  8888776543 23 5


Q ss_pred             ceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE------EEEEEccCc
Q 005812          467 KGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ------LTVLKALDK  510 (676)
Q Consensus       467 ~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~------l~v~~a~~k  510 (676)
                      +++|||+|.+.++|.+|+..||     +..|.|+.      |+|.++.++
T Consensus       436 ~~~gfVeF~~~e~A~~Al~~ln-----~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       436 SKMGLLEWESVEDAVEALIALN-----HHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             ceeEEEEcCCHHHHHHHHHHhc-----CCccCCCCCCccceEEEEeccCC
Confidence            8999999999999999999999     99999985      999998764

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=8.5e-40  Score=339.05  Aligned_cols=345  Identities=22%  Similarity=0.277  Sum_probs=283.6

Q ss_pred             EEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeEE
Q 005812          123 TVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTV  202 (676)
Q Consensus       123 ~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~i  202 (676)
                      .||||   +++|+..|+++|+.+|+|.++++..|          . + +.|||||.|.++++|.+|+.++|...+.|+.|
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d----------~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~   67 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRD----------A-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPI   67 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeec----------C-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEE
Confidence            48999   99999999999999999999998865          3 4 89999999999999999999999999999999


Q ss_pred             EEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCce
Q 005812          203 WARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK  282 (676)
Q Consensus       203 ~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~  282 (676)
                      ++........     .|||+||+++++...|.++|+.||.|.+|++.++. .| ++|| ||+|.++++|++|+..+||..
T Consensus        68 rim~s~rd~~-----~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~l  139 (369)
T KOG0123|consen   68 RIMWSQRDPS-----LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGML  139 (369)
T ss_pred             EeehhccCCc-----eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcc
Confidence            9976543222     39999999999999999999999999999999986 44 9999 999999999999999999999


Q ss_pred             eCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhh
Q 005812          283 FGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLN  362 (676)
Q Consensus       283 ~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  362 (676)
                      +.|+.|.|....++.........                                                         
T Consensus       140 l~~kki~vg~~~~~~er~~~~~~---------------------------------------------------------  162 (369)
T KOG0123|consen  140 LNGKKIYVGLFERKEEREAPLGE---------------------------------------------------------  162 (369)
T ss_pred             cCCCeeEEeeccchhhhcccccc---------------------------------------------------------
Confidence            99999999988665432211110                                                         


Q ss_pred             cccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHH
Q 005812          363 KLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEV  442 (676)
Q Consensus       363 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl  442 (676)
                                                                                ....-..++++|++.+++++.|
T Consensus       163 ----------------------------------------------------------~~~~~t~v~vk~~~~~~~~~~l  184 (369)
T KOG0123|consen  163 ----------------------------------------------------------YKKRFTNVYVKNLEEDSTDEEL  184 (369)
T ss_pred             ----------------------------------------------------------hhhhhhhhheeccccccchHHH
Confidence                                                                      0001257999999999999999


Q ss_pred             HHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhhhHhhhhhc
Q 005812          443 KQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSK  522 (676)
Q Consensus       443 ~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~~~~~~~~~  522 (676)
                      .++|+.+|.|.++.++.+. .+.++||+||.|.++++|..|+..|+     +..++|..+.|..+..+.+....-.++  
T Consensus       185 ~~~f~~~g~i~s~~v~~~~-~g~~~~~gfv~f~~~e~a~~av~~l~-----~~~~~~~~~~V~~aqkk~e~~~~l~~~--  256 (369)
T KOG0123|consen  185 KDLFSAYGSITSVAVMRDS-IGKSKGFGFVNFENPEDAKKAVETLN-----GKIFGDKELYVGRAQKKSEREAELKRK--  256 (369)
T ss_pred             HHhhcccCcceEEEEeecC-CCCCCCccceeecChhHHHHHHHhcc-----CCcCCccceeecccccchhhHHHHhhh--
Confidence            9999999999999988885 56699999999999999999999999     999999999999988743322111111  


Q ss_pred             ccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCeEEEecCCcccCHHHHHHHHHHHH
Q 005812          523 NETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAV  602 (676)
Q Consensus       523 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~V~nlp~~~te~~l~~~F~~~~  602 (676)
                                                               ..+....+........|||+|++..++.+.|+..|+   
T Consensus       257 -----------------------------------------~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~---  292 (369)
T KOG0123|consen  257 -----------------------------------------FEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFS---  292 (369)
T ss_pred             -----------------------------------------hHhhhhhccccccccccccccCccccchhHHHHHHh---
Confidence                                                     000011111122346799999999999999999999   


Q ss_pred             HhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCCCCCcccCccccccc
Q 005812          603 VSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAADAQ  673 (676)
Q Consensus       603 ~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~~~~~~~~~~~~~~~  673 (676)
                            .||.|.+++|+.++.       ++++|+|||+|.+.++|.+|+..+||. ++-+  +.+.|+.+|
T Consensus       293 ------~~GeI~s~kv~~~~~-------g~skG~gfV~fs~~eeA~~A~~~~n~~-~i~~--k~l~vav~q  347 (369)
T KOG0123|consen  293 ------SFGEITSAKVMVDEN-------GKSKGFGFVEFSSPEEAKKAMTEMNGR-LIGG--KPLYVAVAQ  347 (369)
T ss_pred             ------cccceeeEEEEeccC-------CCccceEEEEcCCHHHHHHHHHhhChh-hhcC--CchhhhHHh
Confidence                  599999999998854       689999999999999999999999994 4323  344444443

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=100.00  E-value=1.3e-39  Score=351.98  Aligned_cols=245  Identities=24%  Similarity=0.331  Sum_probs=208.1

Q ss_pred             cCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeec-
Q 005812          120 VARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIK-  198 (676)
Q Consensus       120 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~-  198 (676)
                      .+++|||+|||+++++++|+++|++||.|.+++|++|.          +|+++|||||+|.+.++|.+|++.||+..+. 
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~----------sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~  126 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDF----------SGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRP  126 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECC----------CCCccceEEEEeCCHHHHHHHHHHcCCCeecC
Confidence            45789999999999999999999999999999999772          4899999999999999999999999999886 


Q ss_pred             CeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCc-eEEEEE-cccCCCCCceeEEEEEecCHHHHHHHHH
Q 005812          199 GGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGL-VWNVYI-PHNTDTGLSKGFAFVKFTCKRDAESAIQ  276 (676)
Q Consensus       199 ~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~-i~~v~i-~~~~~~~~~~g~afV~f~~~~~A~~A~~  276 (676)
                      |+.+.+..      ....++|||+|||.++++++|.++|++++. +.++.+ ......++++|||||+|.+.++|..|++
T Consensus       127 Gr~l~V~~------S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~Air  200 (578)
T TIGR01648       127 GRLLGVCI------SVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARR  200 (578)
T ss_pred             Cccccccc------cccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHH
Confidence            67776653      235789999999999999999999999864 444444 3333456789999999999999999999


Q ss_pred             HhCC--ceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHH
Q 005812          277 KFNG--QKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEV  354 (676)
Q Consensus       277 ~l~~--~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  354 (676)
                      .|+.  ..+.|+.|.|.|+.+......                                                     
T Consensus       201 kL~~gki~l~Gr~I~VdwA~p~~~~d~-----------------------------------------------------  227 (578)
T TIGR01648       201 KLMPGRIQLWGHVIAVDWAEPEEEVDE-----------------------------------------------------  227 (578)
T ss_pred             HhhccceEecCceEEEEeecccccccc-----------------------------------------------------
Confidence            8864  357899999999976431000                                                     


Q ss_pred             HHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCC
Q 005812          355 DIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLP  434 (676)
Q Consensus       355 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp  434 (676)
                                                                                       ......++|||+|||
T Consensus       228 -----------------------------------------------------------------~~~~~~k~LfVgNL~  242 (578)
T TIGR01648       228 -----------------------------------------------------------------DVMAKVKILYVRNLM  242 (578)
T ss_pred             -----------------------------------------------------------------cccccccEEEEeCCC
Confidence                                                                             000113689999999


Q ss_pred             CCCCHHHHHHHHHhC--CceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCch
Q 005812          435 FDLDNEEVKQRFSAF--GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       435 ~~~teedl~~~F~~~--G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~  511 (676)
                      +.+++++|+++|+.|  |.|..|.++        ++||||+|.+.++|.+|++.||     +..|+|+.|.|.|+.++.
T Consensus       243 ~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~ln-----G~~i~Gr~I~V~~Akp~~  308 (578)
T TIGR01648       243 TTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELN-----GKELEGSEIEVTLAKPVD  308 (578)
T ss_pred             CCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhC-----CCEECCEEEEEEEccCCC
Confidence            999999999999999  999998764        4699999999999999999999     999999999999998764

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=100.00  E-value=2.8e-40  Score=346.41  Aligned_cols=372  Identities=22%  Similarity=0.321  Sum_probs=265.9

Q ss_pred             hhcccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCC
Q 005812          116 QKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQK  195 (676)
Q Consensus       116 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~  195 (676)
                      .+.....+|||.|||+..+++||+.+|                                |||.|..+++|.+|...++|+
T Consensus       222 e~i~etgrlf~RNLpyt~~eed~~~lf--------------------------------a~v~~~~~~~avka~~~~D~k  269 (725)
T KOG0110|consen  222 EDISETGRLFVRNLPYTSTEEDLLKLF--------------------------------AFVTFMFPEHAVKAYSELDGK  269 (725)
T ss_pred             hHHHhhhhhhhccCCccccHHHHHHhh--------------------------------HHHhhhhhHHHHhhhhhcccc
Confidence            445566789999999999999999988                                477788888888888888888


Q ss_pred             eecCeEEEEecCCC-----------------------------------------------------------------C
Q 005812          196 EIKGGTVWARQLGG-----------------------------------------------------------------E  210 (676)
Q Consensus       196 ~~~~~~i~v~~~~~-----------------------------------------------------------------~  210 (676)
                      .+.|+.+.+.+...                                                                 .
T Consensus       270 ~fqgrmlhvlp~~~k~~~~~~~~~~~~~~k~~ke~~rk~~~~~~~~wn~l~~~~~ava~~~a~k~~v~k~~i~d~~~~gs  349 (725)
T KOG0110|consen  270 VFQGRMLHVLPSKEKSTAKEDASELGSDYKKEKELKRKAASASFHSWNTLFMGANAVAGILAQKLGVEKSRILDGSLSGS  349 (725)
T ss_pred             ccccceeeecCcchhhhhhhhHhhcCCcHHHHHHhccccchhcceecccccccccHHHHHHHHHhCCeeeeeechhhcch
Confidence            88888776531000                                                                 0


Q ss_pred             ------------------------------CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeE
Q 005812          211 ------------------------------GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGF  260 (676)
Q Consensus       211 ------------------------------~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~  260 (676)
                                                    ......+.|+|+|||..+..++|..+|..||.|..+.++.   .|   --
T Consensus       350 avr~al~etr~~~e~~~~~ee~gV~l~~F~~~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~---~G---~~  423 (725)
T KOG0110|consen  350 AVRLALGETRVVQEVRRFFEENGVKLDAFSQAERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPP---GG---TG  423 (725)
T ss_pred             HHHHHHHHhhhchhhhhhHHhhCcccccchhhhhhcceeeeccCccccccHHHHHHhhcccccceeecCc---cc---ce
Confidence                                          0122357899999999999999999999999999996663   22   23


Q ss_pred             EEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCcc
Q 005812          261 AFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSE  340 (676)
Q Consensus       261 afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (676)
                      |+|.|.++.+|+.|++.|.+..+...++.+.|+ |...+................               .....+.-..
T Consensus       424 aiv~fl~p~eAr~Afrklaysr~k~~plyle~a-P~dvf~~~pka~~~~~e~~~~---------------~ee~~~Er~s  487 (725)
T KOG0110|consen  424 AIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWA-PEDVFTEDPKADDLSAESRSK---------------MEENPSERVS  487 (725)
T ss_pred             eeeeecCccchHHHHHHhchhhhccCccccccC-hhhhccCCccccccccccccc---------------cccCcceecc
Confidence            999999999999999999999999999999998 544433111000000000000               0000000000


Q ss_pred             ccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccC
Q 005812          341 KEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEG  420 (676)
Q Consensus       341 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  420 (676)
                      ..                         .+.+....+..                  +               .+......
T Consensus       488 ~~-------------------------d~~v~eD~d~t------------------e---------------~ss~a~~a  509 (725)
T KOG0110|consen  488 AE-------------------------DGQVEEDKDPT------------------E---------------ESSLARVA  509 (725)
T ss_pred             cc-------------------------cccccccCCcc------------------c---------------cccchhhh
Confidence            00                         00000000000                  0               00000000


Q ss_pred             CCC-CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHcCCCCCCCee
Q 005812          421 EDE-LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVT---KRPKGTGFLKFKTVEAATAAVSASKTTSGLGIF  496 (676)
Q Consensus       421 ~~~-~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~---~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~  496 (676)
                      ... ..+.|||+||+++++.++|..+|...|.|.++.|.+.+..   -.+.|||||+|.++++|++|++.|+     |+.
T Consensus       510 ~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lq-----gtv  584 (725)
T KOG0110|consen  510 EDEETETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQ-----GTV  584 (725)
T ss_pred             hccccchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhc-----Cce
Confidence            111 1133999999999999999999999999999988766432   2367999999999999999999999     999


Q ss_pred             ecCcEEEEEEccCchhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCcccc
Q 005812          497 LKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVS  576 (676)
Q Consensus       497 l~gr~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~  576 (676)
                      |+||.|.|.++..+.....-   +                                             +..+.+    .
T Consensus       585 ldGH~l~lk~S~~k~~~~~g---K---------------------------------------------~~~~kk----~  612 (725)
T KOG0110|consen  585 LDGHKLELKISENKPASTVG---K---------------------------------------------KKSKKK----K  612 (725)
T ss_pred             ecCceEEEEeccCccccccc---c---------------------------------------------cccccc----c
Confidence            99999999998744322110   0                                             000011    2


Q ss_pred             CCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcC
Q 005812          577 RTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN  656 (676)
Q Consensus       577 ~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng  656 (676)
                      .+.|+|+||||.++..+++.+|.         .||.|.+|+|+...      +.+-++|||||+|.++.+|.+|+.+|. 
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~---------aFGqlksvRlPKK~------~k~a~rGF~Fv~f~t~~ea~nA~~al~-  676 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFT---------AFGQLKSVRLPKKI------GKGAHRGFGFVDFLTPREAKNAFDALG-  676 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHh---------cccceeeeccchhh------cchhhccceeeeccCcHHHHHHHHhhc-
Confidence            37899999999999999999999         69999999999763      345779999999999999999999999 


Q ss_pred             CCCCCCcccCcccccccc
Q 005812          657 NPSKLFYHHCFDAADAQC  674 (676)
Q Consensus       657 ~~~~~~~~~~~~~~~~~~  674 (676)
                      ..++||  ||+++.+|..
T Consensus       677 STHlyG--RrLVLEwA~~  692 (725)
T KOG0110|consen  677 STHLYG--RRLVLEWAKS  692 (725)
T ss_pred             ccceec--hhhheehhcc
Confidence            689999  8888888754

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=6e-39  Score=318.63  Aligned_cols=249  Identities=25%  Similarity=0.324  Sum_probs=218.2

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeec
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIK  198 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~  198 (676)
                      ..++.|||+.||.++.|++|..+|++.|+|.+++||+|+.         +|.++|||||.|.+.++|++|++.||+..|.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~---------sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir  151 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPF---------SGDNRGYAFVTFCTKEEAQEAIKELNNYEIR  151 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeeccc---------CCCCcceEEEEeecHHHHHHHHHHhhCcccc
Confidence            5688999999999999999999999999999999999974         5999999999999999999999999999885


Q ss_pred             -CeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCc-eEEEEEcccCC-CCCceeEEEEEecCHHHHHHHH
Q 005812          199 -GGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGL-VWNVYIPHNTD-TGLSKGFAFVKFTCKRDAESAI  275 (676)
Q Consensus       199 -~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~-i~~v~i~~~~~-~~~~~g~afV~f~~~~~A~~A~  275 (676)
                       |+.|.|.      ....+++|||+|||.++++++|.+.|++.++ |.+|.+...+. ..+++|||||+|.+...|..|.
T Consensus       152 ~GK~igvc------~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aR  225 (506)
T KOG0117|consen  152 PGKLLGVC------VSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMAR  225 (506)
T ss_pred             CCCEeEEE------EeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHH
Confidence             8888886      5567899999999999999999999999876 77777776654 3579999999999999999999


Q ss_pred             HHhCCc--eeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhH
Q 005812          276 QKFNGQ--KFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEE  353 (676)
Q Consensus       276 ~~l~~~--~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  353 (676)
                      ++|-..  .++|+.+.|+|+.|......                                                    
T Consensus       226 rKl~~g~~klwgn~~tVdWAep~~e~de----------------------------------------------------  253 (506)
T KOG0117|consen  226 RKLMPGKIKLWGNAITVDWAEPEEEPDE----------------------------------------------------  253 (506)
T ss_pred             hhccCCceeecCCcceeeccCcccCCCh----------------------------------------------------
Confidence            987654  46899999999988642100                                                    


Q ss_pred             HHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCC
Q 005812          354 VDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNL  433 (676)
Q Consensus       354 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL  433 (676)
                       +                                          .++.                       -+.|||+||
T Consensus       254 -d------------------------------------------~ms~-----------------------VKvLYVRNL  267 (506)
T KOG0117|consen  254 -D------------------------------------------TMSK-----------------------VKVLYVRNL  267 (506)
T ss_pred             -h------------------------------------------hhhh-----------------------eeeeeeecc
Confidence             0                                          0011                       268999999


Q ss_pred             CCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhh
Q 005812          434 PFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLA  513 (676)
Q Consensus       434 p~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~  513 (676)
                      +.++|+|.|+++|+.||.|..|+.++|        ||||.|.+.++|.+||+.+|     |..|+|..|.|.+|++....
T Consensus       268 ~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~n-----gkeldG~~iEvtLAKP~~k~  334 (506)
T KOG0117|consen  268 MESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETN-----GKELDGSPIEVTLAKPVDKK  334 (506)
T ss_pred             chhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhc-----CceecCceEEEEecCChhhh
Confidence            999999999999999999999987644        99999999999999999999     99999999999999986543

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=1.8e-38  Score=293.37  Aligned_cols=315  Identities=23%  Similarity=0.292  Sum_probs=239.7

Q ss_pred             cEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeE
Q 005812          122 RTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGT  201 (676)
Q Consensus       122 ~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~  201 (676)
                      ..|+|--||-.+|++||+.+|...|+|++|++++||-+         |.+.||+||.|.++++|++|+..|||-.+..+.
T Consensus        42 TNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKit---------GqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KT  112 (360)
T KOG0145|consen   42 TNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKIT---------GQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKT  112 (360)
T ss_pred             ceeeeeecccccCHHHHHHHhhcccceeeeeeeecccc---------ccccccceeeecChHHHHHHHhhhcceeeccce
Confidence            35788888999999999999999999999999999854         999999999999999999999999999999999


Q ss_pred             EEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCc
Q 005812          202 VWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQ  281 (676)
Q Consensus       202 i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~  281 (676)
                      |.|....+.........|||.+||..+|..+|..+|++||.|..-+|..|..+|.++|.|||.|...++|+.|++.|||.
T Consensus       113 IKVSyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~  192 (360)
T KOG0145|consen  113 IKVSYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQ  192 (360)
T ss_pred             EEEEeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCC
Confidence            99988777778888899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCC--eeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHH
Q 005812          282 KFGK--RPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARK  359 (676)
Q Consensus       282 ~~~g--~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  359 (676)
                      .-.|  .+|.|.|+...........-.    ..-+...+                        ...+..+.  .  ..+-
T Consensus       193 ~P~g~tepItVKFannPsq~t~~a~ls----~ly~sp~r------------------------r~~Gp~hh--~--~~r~  240 (360)
T KOG0145|consen  193 KPSGCTEPITVKFANNPSQKTNQALLS----QLYQSPAR------------------------RYGGPMHH--Q--AQRF  240 (360)
T ss_pred             CCCCCCCCeEEEecCCcccccchhhhH----HhhcCccc------------------------cCCCcccc--h--hhhh
Confidence            8755  589999985442111000000    00000000                        00000000  0  0000


Q ss_pred             HhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCH
Q 005812          360 VLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDN  439 (676)
Q Consensus       360 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te  439 (676)
                      .+.+...     +.....+..++.....         ..+.++              --.+....+.+|||.||.++++|
T Consensus       241 r~~~~~~-----~~~~~~rfsP~~~d~m---------~~l~~~--------------~lp~~~~~g~ciFvYNLspd~de  292 (360)
T KOG0145|consen  241 RLDNLLN-----PHAAQARFSPMTIDGM---------SGLAGV--------------NLPGGPGGGWCIFVYNLSPDADE  292 (360)
T ss_pred             ccccccc-----hhhhhccCCCcccccc---------ceeeee--------------ccCCCCCCeeEEEEEecCCCchH
Confidence            0000000     0000111111111000         000000              01123344799999999999999


Q ss_pred             HHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCc
Q 005812          440 EEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK  510 (676)
Q Consensus       440 edl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k  510 (676)
                      .-|+++|.+||.|..|+|++|..+++.+|||||.+.+.++|..|+..||     |..+++|.|.|.+...+
T Consensus       293 ~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLN-----Gy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  293 SILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLN-----GYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             hHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhc-----CccccceEEEEEEecCC
Confidence            9999999999999999999999999999999999999999999999999     99999999999996543

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=8.2e-39  Score=331.70  Aligned_cols=313  Identities=23%  Similarity=0.368  Sum_probs=262.7

Q ss_pred             CcccCCCCcccceEEEEecCHHHHHHHHHHhCCceecCeEEEEeeccccchHHHhhhhhchhhhhhhhhhccCCCCCccc
Q 005812            1 MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAEDIEKTMDNKDGVIS   80 (676)
Q Consensus         1 ~v~~~~tg~s~G~afV~F~~~edA~~Al~~~~g~~i~gr~i~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (676)
                      |++|- |  |.|||||.|.+++||++||+.+|...|.|++|+|+|+...                               
T Consensus        30 vc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd-------------------------------   75 (369)
T KOG0123|consen   30 VCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD-------------------------------   75 (369)
T ss_pred             EeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC-------------------------------
Confidence            35666 5  9999999999999999999999999999999999999322                               


Q ss_pred             ccccccchhhccCCCCCCCcccccCcccCCCCccchhcccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhh
Q 005812           81 GAEKHSSKLLESGKTVKPRKAATLGIDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEEL  160 (676)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~  160 (676)
                                                              ...|||.||+++++..+|+++|+.||.|.+|++..+..  
T Consensus        76 ----------------------------------------~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~--  113 (369)
T KOG0123|consen   76 ----------------------------------------PSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN--  113 (369)
T ss_pred             ----------------------------------------CceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC--
Confidence                                                    01289999999999999999999999999999997643  


Q ss_pred             hhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeEEEEecCCCC--------CCCCCCcEEEEcCCCCCCCHHH
Q 005812          161 EQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGE--------GSKTQKWKLIIRNIPFKAKVNE  232 (676)
Q Consensus       161 ~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~i~v~~~~~~--------~~~~~~~~v~V~nLp~~~~e~~  232 (676)
                              | ++|| ||+|.+++.|.+|+..+||..+.|+.|++-.....        ........++|.|++.+.+++.
T Consensus       114 --------g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~  183 (369)
T KOG0123|consen  114 --------G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEE  183 (369)
T ss_pred             --------C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhcccccchhhhhhhhheeccccccchHH
Confidence                    5 8999 99999999999999999999999999998433211        1334567899999999999999


Q ss_pred             HHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCC
Q 005812          233 IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKG  312 (676)
Q Consensus       233 l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~  312 (676)
                      |..+|..||.|.++.++.+. .++++||+||.|.+.++|..|+..|++..+.+..+.|..+..+......          
T Consensus       184 l~~~f~~~g~i~s~~v~~~~-~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~~----------  252 (369)
T KOG0123|consen  184 LKDLFSAYGSITSVAVMRDS-IGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKKSEREAE----------  252 (369)
T ss_pred             HHHhhcccCcceEEEEeecC-CCCCCCccceeecChhHHHHHHHhccCCcCCccceeecccccchhhHHH----------
Confidence            99999999999999999986 5669999999999999999999999999999999999877542211100          


Q ss_pred             CCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchh
Q 005812          313 DGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKT  392 (676)
Q Consensus       313 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  392 (676)
                                                                  +.......                            
T Consensus       253 --------------------------------------------l~~~~~~~----------------------------  260 (369)
T KOG0123|consen  253 --------------------------------------------LKRKFEQE----------------------------  260 (369)
T ss_pred             --------------------------------------------HhhhhHhh----------------------------
Confidence                                                        00000000                            


Q ss_pred             hccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEE
Q 005812          393 VNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFL  472 (676)
Q Consensus       393 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV  472 (676)
                                             ...........+|||+||+..++.+.|+++|+.||.|.+++|+.+. .++++||+||
T Consensus       261 -----------------------~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~-~g~skG~gfV  316 (369)
T KOG0123|consen  261 -----------------------FAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDE-NGKSKGFGFV  316 (369)
T ss_pred             -----------------------hhhccccccccccccccCccccchhHHHHHHhcccceeeEEEEecc-CCCccceEEE
Confidence                                   0000012234689999999999999999999999999999998884 6899999999


Q ss_pred             EeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCch
Q 005812          473 KFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       473 ~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~  511 (676)
                      +|.+.++|.+|+..+|     +..+++++|.|.+++.++
T Consensus       317 ~fs~~eeA~~A~~~~n-----~~~i~~k~l~vav~qr~~  350 (369)
T KOG0123|consen  317 EFSSPEEAKKAMTEMN-----GRLIGGKPLYVAVAQRKE  350 (369)
T ss_pred             EcCCHHHHHHHHHhhC-----hhhhcCCchhhhHHhhhc
Confidence            9999999999999999     999999999999988544

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=3.7e-37  Score=284.67  Aligned_cols=299  Identities=22%  Similarity=0.336  Sum_probs=234.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....+.|+|.-||..+|+++|+.+|...|.|++|++++|+.+|.+-||+||.|.+++||++|+..|||..+..+.|+|.|
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCC
Q 005812          293 AVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLP  372 (676)
Q Consensus       293 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  372 (676)
                      +.|...                                                                          
T Consensus       118 ARPSs~--------------------------------------------------------------------------  123 (360)
T KOG0145|consen  118 ARPSSD--------------------------------------------------------------------------  123 (360)
T ss_pred             ccCChh--------------------------------------------------------------------------
Confidence            987531                                                                          


Q ss_pred             CCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCce
Q 005812          373 SLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEV  452 (676)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v  452 (676)
                                                                       ...+.+|||.+||..+|..||.++|++||.|
T Consensus       124 -------------------------------------------------~Ik~aNLYvSGlPktMtqkelE~iFs~fGrI  154 (360)
T KOG0145|consen  124 -------------------------------------------------SIKDANLYVSGLPKTMTQKELEQIFSPFGRI  154 (360)
T ss_pred             -------------------------------------------------hhcccceEEecCCccchHHHHHHHHHHhhhh
Confidence                                                             1123689999999999999999999999999


Q ss_pred             eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc--EEEEEEccCchhhhhHhhhhhcccccccCc
Q 005812          453 VSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR--QLTVLKALDKKLAHDKEIDKSKNETNDHRN  530 (676)
Q Consensus       453 ~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr--~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~  530 (676)
                      ..-+|+.|..+|.++|.|||.|+...+|..|++.||     |..--|.  +|.|.+|........+...         ..
T Consensus       155 ItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lN-----G~~P~g~tepItVKFannPsq~t~~a~l---------s~  220 (360)
T KOG0145|consen  155 ITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLN-----GQKPSGCTEPITVKFANNPSQKTNQALL---------SQ  220 (360)
T ss_pred             hhhhhhhhcccceecceeEEEecchhHHHHHHHhcc-----CCCCCCCCCCeEEEecCCcccccchhhh---------HH
Confidence            999999999999999999999999999999999999     7666664  8999999876433322111         11


Q ss_pred             ccccccCcccC----------------CCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCeEEEecCCcccCHHHH
Q 005812          531 LYLAKEGLILE----------------GTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGL  594 (676)
Q Consensus       531 ~~~~~~g~~~~----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~V~nlp~~~te~~l  594 (676)
                      +|.+....+..                ........++.....-.     ......-|.......||||.||..+++|.-|
T Consensus       221 ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~-----~l~~~~lp~~~~~g~ciFvYNLspd~de~~L  295 (360)
T KOG0145|consen  221 LYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMS-----GLAGVNLPGGPGGGWCIFVYNLSPDADESIL  295 (360)
T ss_pred             hhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccc-----eeeeeccCCCCCCeeEEEEEecCCCchHhHH
Confidence            12111111000                00000011110000000     0001111333335689999999999999999


Q ss_pred             HHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCCCCCcccCccccc
Q 005812          595 KKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAAD  671 (676)
Q Consensus       595 ~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~~~~~~~~~~~~~  671 (676)
                      -++|.         +||.|..|++++|..+      +.++|||||.+.+.++|.-||..|||+.+   ..+.++|+.
T Consensus       296 WQlFg---------pFGAv~nVKvirD~tt------nkCKGfgFVtMtNYdEAamAi~sLNGy~l---g~rvLQVsF  354 (360)
T KOG0145|consen  296 WQLFG---------PFGAVTNVKVIRDFTT------NKCKGFGFVTMTNYDEAAMAIASLNGYRL---GDRVLQVSF  354 (360)
T ss_pred             HHHhC---------cccceeeEEEEecCCc------ccccceeEEEecchHHHHHHHHHhcCccc---cceEEEEEE
Confidence            99999         7999999999999876      48999999999999999999999999854   245566653

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=1.5e-36  Score=301.66  Aligned_cols=269  Identities=23%  Similarity=0.310  Sum_probs=221.9

Q ss_pred             eCCHHHHHHHHHHhCCCeecCeEEEEecCCC------CCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccC
Q 005812          179 YTTVKSACASVALLHQKEIKGGTVWARQLGG------EGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNT  252 (676)
Q Consensus       179 F~~~~~A~~A~~~l~~~~~~~~~i~v~~~~~------~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~  252 (676)
                      ..+.++|.+||..-.+..+.-..- -+...+      .......+.|||+.||.++.|++|.-+|++.|.|.+++|++++
T Consensus        41 ~~~~eaal~al~E~tgy~l~ve~g-qrk~ggPpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~  119 (506)
T KOG0117|consen   41 VQSEEAALKALLERTGYTLVVENG-QRKYGGPPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDP  119 (506)
T ss_pred             cccHHHHHHHHHHhcCceEEEecc-ccccCCCCCcccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecc
Confidence            445788888887655543321000 011111      1233567999999999999999999999999999999999999


Q ss_pred             CCCCceeEEEEEecCHHHHHHHHHHhCCcee-CCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccc
Q 005812          253 DTGLSKGFAFVKFTCKRDAESAIQKFNGQKF-GKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAET  331 (676)
Q Consensus       253 ~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~-~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  331 (676)
                      .+|.++|||||.|++.++|+.|++.||+..| .|+.|.|+.+..                                    
T Consensus       120 ~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Sva------------------------------------  163 (506)
T KOG0117|consen  120 FSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVA------------------------------------  163 (506)
T ss_pred             cCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeee------------------------------------
Confidence            9999999999999999999999999999998 589999998743                                    


Q ss_pred             cCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCC
Q 005812          332 ASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSK  411 (676)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  411 (676)
                                                                                                      
T Consensus       164 --------------------------------------------------------------------------------  163 (506)
T KOG0117|consen  164 --------------------------------------------------------------------------------  163 (506)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCc-eeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHcCC
Q 005812          412 PKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGE-VVSFVPVLHQ-VTKRPKGTGFLKFKTVEAATAAVSASKT  489 (676)
Q Consensus       412 ~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~-v~~v~i~~~~-~~~~~~g~afV~F~t~~~A~~Al~~l~~  489 (676)
                                   +++|||+|||..+++++|.+.|++.+. |+.|.+.... +..+.+|||||+|.++..|..|.++|-.
T Consensus       164 -------------n~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~  230 (506)
T KOG0117|consen  164 -------------NCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMP  230 (506)
T ss_pred             -------------cceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccC
Confidence                         379999999999999999999999873 7777665543 3567899999999999999999999873


Q ss_pred             CCCCCeeecCcEEEEEEccCchhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCC
Q 005812          490 TSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQ  569 (676)
Q Consensus       490 ~~~~g~~l~gr~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  569 (676)
                         +.+.+.|+.+.|+||.+..+.......                                                  
T Consensus       231 ---g~~klwgn~~tVdWAep~~e~ded~ms--------------------------------------------------  257 (506)
T KOG0117|consen  231 ---GKIKLWGNAITVDWAEPEEEPDEDTMS--------------------------------------------------  257 (506)
T ss_pred             ---CceeecCCcceeeccCcccCCChhhhh--------------------------------------------------
Confidence               379999999999999886533211000                                                  


Q ss_pred             CCCccccCCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHH
Q 005812          570 SPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALV  649 (676)
Q Consensus       570 ~p~~~~~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~  649 (676)
                            .-..||||||+.++|++.|+++|.         .||.|.+|+.++|              ||||+|.+.++|++
T Consensus       258 ------~VKvLYVRNL~~~tTeE~lk~~F~---------~~G~veRVkk~rD--------------YaFVHf~eR~davk  308 (506)
T KOG0117|consen  258 ------KVKVLYVRNLMESTTEETLKKLFN---------EFGKVERVKKPRD--------------YAFVHFAEREDAVK  308 (506)
T ss_pred             ------heeeeeeeccchhhhHHHHHHHHH---------hccceEEeecccc--------------eeEEeecchHHHHH
Confidence                  114699999999999999999999         5999999999866              99999999999999


Q ss_pred             HHHHHcCCCC
Q 005812          650 ALRVLNNNPS  659 (676)
Q Consensus       650 Ai~~lng~~~  659 (676)
                      ||+.+||+-+
T Consensus       309 Am~~~ngkel  318 (506)
T KOG0117|consen  309 AMKETNGKEL  318 (506)
T ss_pred             HHHHhcCcee
Confidence            9999999655

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=100.00  E-value=3.4e-36  Score=325.52  Aligned_cols=278  Identities=21%  Similarity=0.260  Sum_probs=219.8

Q ss_pred             CHHHHHHHHHHhCCCeecCeEEEEecCCC-----CCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCC
Q 005812          181 TVKSACASVALLHQKEIKGGTVWARQLGG-----EGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTG  255 (676)
Q Consensus       181 ~~~~A~~A~~~l~~~~~~~~~i~v~~~~~-----~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~  255 (676)
                      ..+.|.+|+..++|..+.........-.+     .......++|||+|||.+++|++|+++|+.||.|.+|+|+++ .+|
T Consensus        18 ~~~~a~~a~~~~~gy~~~~~~g~r~~g~Pp~~~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG   96 (578)
T TIGR01648        18 PDEAALKALLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSG   96 (578)
T ss_pred             ccHHHHHHHHHhhCccccccCCcccCCCCCCcccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCC
Confidence            46889999998888776544332211111     112345689999999999999999999999999999999999 789


Q ss_pred             CceeEEEEEecCHHHHHHHHHHhCCceeC-CeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCC
Q 005812          256 LSKGFAFVKFTCKRDAESAIQKFNGQKFG-KRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASD  334 (676)
Q Consensus       256 ~~~g~afV~f~~~~~A~~A~~~l~~~~~~-g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  334 (676)
                      +++|||||+|.+.++|++||+.||+..+. |+.|.|.++..                                       
T Consensus        97 ~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~~---------------------------------------  137 (578)
T TIGR01648        97 QNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVD---------------------------------------  137 (578)
T ss_pred             CccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccccc---------------------------------------
Confidence            99999999999999999999999999885 67777765421                                       


Q ss_pred             CCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCC
Q 005812          335 DSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKS  414 (676)
Q Consensus       335 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  414 (676)
                                                                                                      
T Consensus       138 --------------------------------------------------------------------------------  137 (578)
T TIGR01648       138 --------------------------------------------------------------------------------  137 (578)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCc-eeEEEEee-cCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCC
Q 005812          415 LKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGE-VVSFVPVL-HQVTKRPKGTGFLKFKTVEAATAAVSASKTTSG  492 (676)
Q Consensus       415 ~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~-v~~v~i~~-~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~  492 (676)
                                .++|||+|||..+++++|.++|++++. +..+.++. ....++++|||||+|.++++|..|+..|+..  
T Consensus       138 ----------~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~g--  205 (578)
T TIGR01648       138 ----------NCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPG--  205 (578)
T ss_pred             ----------CceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhcc--
Confidence                      268999999999999999999999863 44443332 2335678999999999999999999988621  


Q ss_pred             CCeeecCcEEEEEEccCchhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCC
Q 005812          493 LGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPN  572 (676)
Q Consensus       493 ~g~~l~gr~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~  572 (676)
                       .+.+.|+.|.|.|+.+......                                                        .
T Consensus       206 -ki~l~Gr~I~VdwA~p~~~~d~--------------------------------------------------------~  228 (578)
T TIGR01648       206 -RIQLWGHVIAVDWAEPEEEVDE--------------------------------------------------------D  228 (578)
T ss_pred             -ceEecCceEEEEeecccccccc--------------------------------------------------------c
Confidence             4678999999999876432110                                                        0


Q ss_pred             ccccCCeEEEecCCcccCHHHHHHHHHHHHHhhhcccC--CCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHH
Q 005812          573 FHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQK--PVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVA  650 (676)
Q Consensus       573 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~--G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~A  650 (676)
                      ......+|||+|||.++|+++|+++|+         .|  |.|.+|+++              ++||||+|.++++|.+|
T Consensus       229 ~~~~~k~LfVgNL~~~~tee~L~~~F~---------~f~~G~I~rV~~~--------------rgfAFVeF~s~e~A~kA  285 (578)
T TIGR01648       229 VMAKVKILYVRNLMTTTTEEIIEKSFS---------EFKPGKVERVKKI--------------RDYAFVHFEDREDAVKA  285 (578)
T ss_pred             ccccccEEEEeCCCCCCCHHHHHHHHH---------hcCCCceEEEEee--------------cCeEEEEeCCHHHHHHH
Confidence            000225899999999999999999999         48  999999776              56999999999999999


Q ss_pred             HHHHcCCCCCCCcccCccccccc
Q 005812          651 LRVLNNNPSKLFYHHCFDAADAQ  673 (676)
Q Consensus       651 i~~lng~~~~~~~~~~~~~~~~~  673 (676)
                      |+.|||.. +.+  +++.|+.|.
T Consensus       286 i~~lnG~~-i~G--r~I~V~~Ak  305 (578)
T TIGR01648       286 MDELNGKE-LEG--SEIEVTLAK  305 (578)
T ss_pred             HHHhCCCE-ECC--EEEEEEEcc
Confidence            99999963 323  566666553

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=4e-36  Score=304.66  Aligned_cols=319  Identities=24%  Similarity=0.316  Sum_probs=224.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      .+|||++||+.++.++|.++|+.+|+|..+.++.++.++.++|||||.|.-.+++++|+..+++..|.|+.|.|.++.++
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            79999999999999999999999999999999999988899999999999999999999999999999999999999776


Q ss_pred             CCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCC
Q 005812          297 NIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSD  376 (676)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  376 (676)
                      .........   .+                             +                   .+....           
T Consensus        86 ~r~e~~~~~---e~-----------------------------~-------------------~veK~~-----------  103 (678)
T KOG0127|consen   86 ARSEEVEKG---EN-----------------------------K-------------------AVEKPI-----------  103 (678)
T ss_pred             ccchhcccc---cc-----------------------------h-------------------hhhccc-----------
Confidence            432100000   00                             0                   000000           


Q ss_pred             ccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCccc-CCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEE
Q 005812          377 DSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTE-GEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSF  455 (676)
Q Consensus       377 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v  455 (676)
                                                          ...++.. ....+...|.|+||||.+.+.+|+.+|+.||.|..|
T Consensus       104 ------------------------------------~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei  147 (678)
T KOG0127|consen  104 ------------------------------------EQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEI  147 (678)
T ss_pred             ------------------------------------ccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEE
Confidence                                                0000000 011224789999999999999999999999999999


Q ss_pred             EEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhhhHh------hhhhcc-c----
Q 005812          456 VPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKE------IDKSKN-E----  524 (676)
Q Consensus       456 ~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~~~~------~~~~~~-~----  524 (676)
                      .|++.. .|..+|||||.|....+|..|+..+|     +..|+||+|-|.||.+++......      .++... +    
T Consensus       148 ~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N-----~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e  221 (678)
T KOG0127|consen  148 VIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFN-----GNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKE  221 (678)
T ss_pred             EcccCC-CCCccceEEEEEeeHHHHHHHHHhcc-----CceecCceeEEeeecccccccccchhhhhhhhhccchhhhcc
Confidence            888664 56667999999999999999999999     999999999999999998655421      111110 0    


Q ss_pred             -ccccCcccccccCcccCCCCCCCCC----------------ChhHHHHHHHHHHHHhhcCCC-CCccccCCeEEEecCC
Q 005812          525 -TNDHRNLYLAKEGLILEGTPAAEGV----------------SDDDMSKRQMLHEKKMTKLQS-PNFHVSRTRLVIYNLP  586 (676)
Q Consensus       525 -~~~~~~~~~~~~g~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~~~~~-p~~~~~~~~l~V~nlp  586 (676)
                       ..+..+-....+|.......-..++                +..+.+.+......+...... +....-..+|||||||
T Consensus       222 ~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~  301 (678)
T KOG0127|consen  222 ADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLP  301 (678)
T ss_pred             cccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCC
Confidence             0011111111111100000000000                000000000000000000000 1111123689999999


Q ss_pred             cccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHH
Q 005812          587 KSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVL  654 (676)
Q Consensus       587 ~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~l  654 (676)
                      |++|+++|.+.|+         +||.|..+.|+.++.|+      +|+|.|||.|.++.+|..||...
T Consensus       302 fD~tEEel~~~fs---------kFG~v~ya~iV~~k~T~------~skGtAFv~Fkt~~~~~~ci~~A  354 (678)
T KOG0127|consen  302 FDTTEEELKEHFS---------KFGEVKYAIIVKDKDTG------HSKGTAFVKFKTQIAAQNCIEAA  354 (678)
T ss_pred             ccccHHHHHHHHH---------hhccceeEEEEeccCCC------CcccceEEEeccHHHHHHHHHhc
Confidence            9999999999999         69999999999999886      99999999999999999999988

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=100.00  E-value=2.7e-34  Score=315.90  Aligned_cols=337  Identities=21%  Similarity=0.305  Sum_probs=226.2

Q ss_pred             cccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCee
Q 005812          118 QRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEI  197 (676)
Q Consensus       118 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~  197 (676)
                      .+..++|||+|||..+++++|+++|+.||.|..|.++.++.         .|+++|||||+|.+.++|.+|+. |+|..+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~---------~~~skg~afVeF~~~e~A~~Al~-l~g~~~  155 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRN---------SRRSKGVAYVEFYDVESVIKALA-LTGQML  155 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC---------CCCcceEEEEEECCHHHHHHHHH-hCCCEE
Confidence            35678999999999999999999999999999999998764         48899999999999999999997 999999


Q ss_pred             cCeEEEEecCCCC------------CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEe
Q 005812          198 KGGTVWARQLGGE------------GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKF  265 (676)
Q Consensus       198 ~~~~i~v~~~~~~------------~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f  265 (676)
                      .|+.|.+......            ......++|||+|||..+++++|+++|+.||.|..|.++.+..+|.++|||||+|
T Consensus       156 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f  235 (457)
T TIGR01622       156 LGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQF  235 (457)
T ss_pred             CCeeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEE
Confidence            9999988643211            1112358999999999999999999999999999999999988889999999999


Q ss_pred             cCHHHHHHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCC
Q 005812          266 TCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLP  345 (676)
Q Consensus       266 ~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  345 (676)
                      .+.++|..|+..|+|..|.|+.|.|.|+...........   ..........                          ..
T Consensus       236 ~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~---~~~~~~~~~~--------------------------~~  286 (457)
T TIGR01622       236 HDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAAN---TFEDIDKQQQ--------------------------MG  286 (457)
T ss_pred             CCHHHHHHHHHhcCCcEECCEEEEEEEccCCCccccchh---hhcccccccc--------------------------CC
Confidence            999999999999999999999999999863221111000   0000000000                          00


Q ss_pred             CCCCchhHHHHHHHHhhccccc-CCCCCCCCCccccccCCCCCCCchhhccccccccccccCC--CCCCCCCCCcccCCC
Q 005812          346 SNADFDEEVDIARKVLNKLTST-TGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNS--SKSKPKSLKQTEGED  422 (676)
Q Consensus       346 ~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~  422 (676)
                      .... ......+...+...... .+.+++............     .......... ..+...  .........+.....
T Consensus       287 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  359 (457)
T TIGR01622       287 KNLN-TEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQ-----RDGIIDPNIP-SRYATGALAIMARNSFVPSTNNN  359 (457)
T ss_pred             cCCC-ccchHHHHHhhccCCCCccccCCCccchhhhhcccc-----cccccccccc-ccccccccccccCCCCCCcccCC
Confidence            0000 00000111111110000 000110000000000000     0000000000 000000  000000111111133


Q ss_pred             CCCCeEEEcCCCCCCC----------HHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCC
Q 005812          423 ELQNTIFICNLPFDLD----------NEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSG  492 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~t----------eedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~  492 (676)
                      .++.+|+|.||....+          .+||++.|++||.|..|.|..    ..+.|++||+|.+.++|.+|++.||    
T Consensus       360 ~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~----~~~~G~~fV~F~~~e~A~~A~~~ln----  431 (457)
T TIGR01622       360 LATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDT----KNSAGKIYLKFSSVDAALAAFQALN----  431 (457)
T ss_pred             CCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeC----CCCceeEEEEECCHHHHHHHHHHhc----
Confidence            5678999999955443          378999999999999997753    3457999999999999999999999    


Q ss_pred             CCeeecCcEEEEEEccC
Q 005812          493 LGIFLKGRQLTVLKALD  509 (676)
Q Consensus       493 ~g~~l~gr~l~v~~a~~  509 (676)
                       |..|+||.|.+.+...
T Consensus       432 -Gr~f~gr~i~~~~~~~  447 (457)
T TIGR01622       432 -GRYFGGKMITAAFVVN  447 (457)
T ss_pred             -CcccCCeEEEEEEEcH
Confidence             9999999999999754

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=100.00  E-value=1.9e-34  Score=317.03  Aligned_cols=317  Identities=24%  Similarity=0.347  Sum_probs=215.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.++.+++++|||||+|.+.++|.+||. |+|..+.|+.|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            3456799999999999999999999999999999999999999999999999999999999998 899999999999987


Q ss_pred             ecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCC
Q 005812          293 AVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLP  372 (676)
Q Consensus       293 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  372 (676)
                      +...........            .                                                .      
T Consensus       165 ~~~~~~~~~~~~------------~------------------------------------------------~------  178 (457)
T TIGR01622       165 SQAEKNRAAKAA------------T------------------------------------------------H------  178 (457)
T ss_pred             cchhhhhhhhcc------------c------------------------------------------------c------
Confidence            643211000000            0                                                0      


Q ss_pred             CCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCce
Q 005812          373 SLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEV  452 (676)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v  452 (676)
                                                .                   .......++|||+|||+.+++++|+++|+.||.|
T Consensus       179 --------------------------~-------------------~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i  213 (457)
T TIGR01622       179 --------------------------Q-------------------PGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDI  213 (457)
T ss_pred             --------------------------c-------------------CCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCe
Confidence                                      0                   0000114799999999999999999999999999


Q ss_pred             eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhhhHhhhhhcccc--cccCc
Q 005812          453 VSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNET--NDHRN  530 (676)
Q Consensus       453 ~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~~~~~~~~~~~~--~~~~~  530 (676)
                      ..|.++.+..+|.++|||||+|.+.++|.+|+..||     |..|.|++|.|.|+..................  ....+
T Consensus       214 ~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~-----g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~  288 (457)
T TIGR01622       214 EDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMN-----GFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKN  288 (457)
T ss_pred             EEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcC-----CcEECCEEEEEEEccCCCccccchhhhccccccccCCcC
Confidence            999999998888999999999999999999999999     99999999999997743211111000000000  00000


Q ss_pred             cc----------cccc----CcccCCCCC-C---CCCChhHHHH---------HHHHHHHHhhcCCCCCccccCCeEEEe
Q 005812          531 LY----------LAKE----GLILEGTPA-A---EGVSDDDMSK---------RQMLHEKKMTKLQSPNFHVSRTRLVIY  583 (676)
Q Consensus       531 ~~----------~~~~----g~~~~~~~~-~---~~~~~~~~~~---------~~~~~~~~~~~~~~p~~~~~~~~l~V~  583 (676)
                      +.          +...    +...++... .   ..+.......         ...........++..+...+..+|+|.
T Consensus       289 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~  368 (457)
T TIGR01622       289 LNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLS  368 (457)
T ss_pred             CCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEe
Confidence            00          0000    000000000 0   0000000000         000000000111111133456789999


Q ss_pred             cCCc--ccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCC
Q 005812          584 NLPK--SMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNN  657 (676)
Q Consensus       584 nlp~--~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~  657 (676)
                      ||..  ...+..+...|.+.+..+|. +||.|..|.|...          .+.|++||+|.++++|.+|++.|||.
T Consensus       369 n~~~~~~~~~~~~~~~~~~dv~~e~~-k~G~v~~v~v~~~----------~~~G~~fV~F~~~e~A~~A~~~lnGr  433 (457)
T TIGR01622       369 NMFDPATEEEPNFDNEILDDVKEECS-KYGGVVHIYVDTK----------NSAGKIYLKFSSVDAALAAFQALNGR  433 (457)
T ss_pred             cCCCCcccccchHHHHHHHHHHHHHH-hcCCeeEEEEeCC----------CCceeEEEEECCHHHHHHHHHHhcCc
Confidence            9943  33334444444445555555 5999999988743          46799999999999999999999997

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=100.00  E-value=2.6e-33  Score=303.16  Aligned_cols=181  Identities=25%  Similarity=0.424  Sum_probs=156.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ...++|||+|||+.+++++|+++|..||.|.+|.|+.++.+|+++|||||+|.+.++|++|++.|||..|.|+.|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999854


Q ss_pred             cCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCC
Q 005812          294 VPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPS  373 (676)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  373 (676)
                      ........         ..    +                               .                        
T Consensus       185 ~~~p~a~~---------~~----~-------------------------------~------------------------  196 (612)
T TIGR01645       185 SNMPQAQP---------II----D-------------------------------M------------------------  196 (612)
T ss_pred             cccccccc---------cc----c-------------------------------c------------------------
Confidence            22110000         00    0                               0                        


Q ss_pred             CCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCcee
Q 005812          374 LSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVV  453 (676)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~  453 (676)
                                                                  ........++|||+|||+++++++|+++|+.||.|.
T Consensus       197 --------------------------------------------~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~  232 (612)
T TIGR01645       197 --------------------------------------------VQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIV  232 (612)
T ss_pred             --------------------------------------------ccccccccceEEeecCCCCCCHHHHHHHHhhcCCee
Confidence                                                        000111236899999999999999999999999999


Q ss_pred             EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCch
Q 005812          454 SFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       454 ~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~  511 (676)
                      +++|+++..++.++|||||+|.+.++|.+|+..||     ++.|+|+.|.|.++.++.
T Consensus       233 svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amN-----g~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       233 KCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN-----LFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             EEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhC-----CCeeCCeEEEEEecCCCc
Confidence            99999998889999999999999999999999999     999999999999998754

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=100.00  E-value=2.9e-33  Score=312.15  Aligned_cols=277  Identities=21%  Similarity=0.248  Sum_probs=211.0

Q ss_pred             hcccCcEEEEcCCCccccHHHHHHHhhcC------------CCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHH
Q 005812          117 KQRVARTVIIGGLLNADMAEEVHRLAGSI------------GTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKS  184 (676)
Q Consensus       117 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~------------G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~  184 (676)
                      ..+..++|||+|||+.+++++|+++|..+            +.|..+.+               ++.+|||||+|.+.++
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~---------------~~~kg~afVeF~~~e~  235 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI---------------NKEKNFAFLEFRTVEE  235 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE---------------CCCCCEEEEEeCCHHH
Confidence            34567899999999999999999999975            23444432               4568999999999999


Q ss_pred             HHHHHHHhCCCeecCeEEEEecCCCCC-----------------------------CCCCCcEEEEcCCCCCCCHHHHHH
Q 005812          185 ACASVALLHQKEIKGGTVWARQLGGEG-----------------------------SKTQKWKLIIRNIPFKAKVNEIKD  235 (676)
Q Consensus       185 A~~A~~~l~~~~~~~~~i~v~~~~~~~-----------------------------~~~~~~~v~V~nLp~~~~e~~l~~  235 (676)
                      |..||+ |+|..|.|..|.+.......                             .....++|||+|||..+++++|++
T Consensus       236 A~~Al~-l~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~  314 (509)
T TIGR01642       236 ATFAMA-LDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKE  314 (509)
T ss_pred             Hhhhhc-CCCeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHH
Confidence            999995 99999999999885321100                             112347999999999999999999


Q ss_pred             hhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCC
Q 005812          236 MFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGN  315 (676)
Q Consensus       236 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~  315 (676)
                      +|+.||.|..+.|+.+..+|.++|||||+|.+.++|..|+..|+|..|.|+.|.|.++..............        
T Consensus       315 ~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~--------  386 (509)
T TIGR01642       315 LLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNG--------  386 (509)
T ss_pred             HHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCcccccc--------
Confidence            999999999999999988999999999999999999999999999999999999999854321000000000        


Q ss_pred             CCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhcc
Q 005812          316 SDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNE  395 (676)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  395 (676)
                       .                          .+..                      ......     ..             
T Consensus       387 -~--------------------------~~~~----------------------~~~~~~-----~~-------------  399 (509)
T TIGR01642       387 -M--------------------------APVT----------------------LLAKAL-----SQ-------------  399 (509)
T ss_pred             -c--------------------------cccc----------------------cccccc-----hh-------------
Confidence             0                          0000                      000000     00             


Q ss_pred             ccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCC----------CHHHHHHHHHhCCceeEEEEeecC---C
Q 005812          396 SAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDL----------DNEEVKQRFSAFGEVVSFVPVLHQ---V  462 (676)
Q Consensus       396 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~----------teedl~~~F~~~G~v~~v~i~~~~---~  462 (676)
                        ...                  .....++.+|+|.||...-          ..++|+++|++||.|..|.|+++.   .
T Consensus       400 --~~~------------------~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~  459 (509)
T TIGR01642       400 --SIL------------------QIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRN  459 (509)
T ss_pred             --hhc------------------cccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCC
Confidence              000                  0012245799999996421          236899999999999999988653   2


Q ss_pred             CCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccC
Q 005812          463 TKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALD  509 (676)
Q Consensus       463 ~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~  509 (676)
                      ++...|+|||+|.+.++|.+|+..||     |..|+|+.|.|.|...
T Consensus       460 ~~~~~G~~fV~F~~~e~A~~A~~~ln-----Gr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       460 STPGVGKVFLEYADVRSAEKAMEGMN-----GRKFNDRVVVAAFYGE  501 (509)
T ss_pred             cCCCcceEEEEECCHHHHHHHHHHcC-----CCEECCeEEEEEEeCH
Confidence            34567999999999999999999999     9999999999999653

Members of this subfamily are found in plants, metazoa and fungi.

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

Probab=100.00  E-value=6.6e-34  Score=281.32  Aligned_cols=373  Identities=21%  Similarity=0.322  Sum_probs=237.6

Q ss_pred             cCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCC-eec
Q 005812          120 VARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQK-EIK  198 (676)
Q Consensus       120 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~-~~~  198 (676)
                      ....+||+.||..++|.||+.+|++||.|.+|.|++||.+         |.++|+|||.|.+.++|.+|+.+|++. .|.
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t---------~~s~gcCFv~~~trk~a~~a~~Alhn~ktlp  103 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKST---------GQSKGCCFVKYYTRKEADEAINALHNQKTLP  103 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEEeeccccc---------CcccceEEEEeccHHHHHHHHHHhhcccccC
Confidence            3557999999999999999999999999999999999964         789999999999999999999999775 556


Q ss_pred             CeE--EEEecCCCCCC-CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHH
Q 005812          199 GGT--VWARQLGGEGS-KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI  275 (676)
Q Consensus       199 ~~~--i~v~~~~~~~~-~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~  275 (676)
                      |..  |.++....+.. ....++|||+-|+..++|.+|+++|++||.|++|.|.++. .+.++|||||.|.+.+.|..||
T Consensus       104 G~~~pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Ai  182 (510)
T KOG0144|consen  104 GMHHPVQVKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAI  182 (510)
T ss_pred             CCCcceeecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHH
Confidence            654  44554433322 2457899999999999999999999999999999999986 7899999999999999999999


Q ss_pred             HHhCCce-e--CCeeEEEEEecCCCCCCcCCcccCcc-------C--CCCCCCCCCCCCCCCCCcccc--cCCCCCCc--
Q 005812          276 QKFNGQK-F--GKRPIAVDWAVPKNIYSSGGAAAGVQ-------N--KGDGNSDSGSDDDLGDDDAET--ASDDSNSS--  339 (676)
Q Consensus       276 ~~l~~~~-~--~g~~i~v~~a~~~~~~~~~~~~~~~~-------~--~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~--  339 (676)
                      +.|||.. +  +..+|.|.|+++++.+..........       +  .......-...    .....+  +.-.+...  
T Consensus       183 ka~ng~~tmeGcs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l----~~~~~~~~Qq~~~sqn~g  258 (510)
T KOG0144|consen  183 KALNGTQTMEGCSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGAL----SNGYQGPQQQTQQSQNVG  258 (510)
T ss_pred             HhhccceeeccCCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhcc----CcccCchhhhccccCCCc
Confidence            9999986 4  45789999999876544322100000       0  00000000000    000000  00000000  


Q ss_pred             cccCCCCCCCch-hHHH---HHHHH----hhcccccC-----------CCCCCCCCccc---------------------
Q 005812          340 EKEDLPSNADFD-EEVD---IARKV----LNKLTSTT-----------GSLPSLSDDSA---------------------  379 (676)
Q Consensus       340 ~~~~~~~~~~~~-~~~~---~~~~~----~~~~~~~~-----------g~~~~~~~~~~---------------------  379 (676)
                      .-...+.-.... ....   .+...    -.......           +...++.....                     
T Consensus       259 ~l~g~~~L~~l~a~~~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~  338 (510)
T KOG0144|consen  259 TLGGLPPLGPLNATQLQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTF  338 (510)
T ss_pred             ccccccCCCCcchhHHHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcC
Confidence            000000000000 0000   00000    00000000           00000000000                     


Q ss_pred             -----------------------------cccCCCCCCCchhhccccccccc-----------cccCCCCCCCCCCCccc
Q 005812          380 -----------------------------LVKGNKEQDSDKTVNESAKVSDV-----------SKLNSSKSKPKSLKQTE  419 (676)
Q Consensus       380 -----------------------------~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~  419 (676)
                                                   ...+.....-.........++..           ...+.....+.......
T Consensus       339 p~t~~~~n~~~~~a~a~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q  418 (510)
T KOG0144|consen  339 PGTPANYNLAGGMAGAGTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQ  418 (510)
T ss_pred             CCCchhcccccccccccccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCcc
Confidence                                         00000000000000000000000           00000000000111123


Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          420 GEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       420 ~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      -....+..|||.+||-+.-+.+|...|..||.|.+.+++.|+.++.+++|+||.|++..+|..||..||     |+.+++
T Consensus       419 ~eGpeGanlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amn-----gfQig~  493 (510)
T KOG0144|consen  419 VEGPEGANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMN-----GFQIGS  493 (510)
T ss_pred             ccCCCccceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhc-----chhhcc
Confidence            356678899999999999999999999999999999999999999999999999999999999999999     999999


Q ss_pred             cEEEEEEccCch
Q 005812          500 RQLTVLKALDKK  511 (676)
Q Consensus       500 r~l~v~~a~~k~  511 (676)
                      ++|+|...+.+.
T Consensus       494 KrlkVQlk~~~~  505 (510)
T KOG0144|consen  494 KRLKVQLKRDRN  505 (510)
T ss_pred             ccceEEeeeccC
Confidence            999999876653

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=100.00  E-value=2.7e-32  Score=295.34  Aligned_cols=170  Identities=14%  Similarity=0.204  Sum_probs=154.0

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeec
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIK  198 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~  198 (676)
                      ...++|||+|||+++++++|+++|..||.|.+|+++.++.         .|+++|||||+|.+.++|.+|+..|||..+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~---------TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~  175 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPA---------TGKHKGFAFVEYEVPEAAQLALEQMNGQMLG  175 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCC---------CCCcCCeEEEEeCcHHHHHHHHHhcCCeEEe
Confidence            4567999999999999999999999999999999998874         4899999999999999999999999999999


Q ss_pred             CeEEEEecCCCCC-----------CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecC
Q 005812          199 GGTVWARQLGGEG-----------SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC  267 (676)
Q Consensus       199 ~~~i~v~~~~~~~-----------~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~  267 (676)
                      |+.|.|.......           .....++|||+|||.++++++|+++|+.||.|.+|+|++++.+++++|||||+|.+
T Consensus       176 GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~  255 (612)
T TIGR01645       176 GRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNN  255 (612)
T ss_pred             cceeeecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECC
Confidence            9999986432211           11234799999999999999999999999999999999999899999999999999


Q ss_pred             HHHHHHHHHHhCCceeCCeeEEEEEecCCC
Q 005812          268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKN  297 (676)
Q Consensus       268 ~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~  297 (676)
                      .++|.+|+..||+..|+|+.|+|.++.+..
T Consensus       256 ~e~A~kAI~amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       256 LQSQSEAIASMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             HHHHHHHHHHhCCCeeCCeEEEEEecCCCc
Confidence            999999999999999999999999987643

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=3.7e-33  Score=260.34  Aligned_cols=233  Identities=26%  Similarity=0.451  Sum_probs=191.1

Q ss_pred             cCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecC
Q 005812          120 VARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKG  199 (676)
Q Consensus       120 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~  199 (676)
                      ..|||||+||.+++||+-|..||++.|.|..++++.+..-                                        
T Consensus         5 ~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~~----------------------------------------   44 (321)
T KOG0148|consen    5 EPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDELK----------------------------------------   44 (321)
T ss_pred             CCceEEeeccChhhHHHHHHHHHHhccccccceeehhhhc----------------------------------------
Confidence            4579999999999999999999999999999998754210                                        


Q ss_pred             eEEEEecCC--CCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHH
Q 005812          200 GTVWARQLG--GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK  277 (676)
Q Consensus       200 ~~i~v~~~~--~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~  277 (676)
                       .+|.....  .........-|||+.|...++-++|++.|.+||.|.+++|++|..+++++|||||.|.+.++|+.||..
T Consensus        45 -v~wa~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~  123 (321)
T KOG0148|consen   45 -VNWATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQ  123 (321)
T ss_pred             -cccccCcccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHH
Confidence             11111111  111222356799999999999999999999999999999999999999999999999999999999999


Q ss_pred             hCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHH
Q 005812          278 FNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIA  357 (676)
Q Consensus       278 l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  357 (676)
                      |||..|++|.|+-.|+..+..-..     ..                                      ...|+      
T Consensus       124 MnGqWlG~R~IRTNWATRKp~e~n-----~~--------------------------------------~ltfd------  154 (321)
T KOG0148|consen  124 MNGQWLGRRTIRTNWATRKPSEMN-----GK--------------------------------------PLTFD------  154 (321)
T ss_pred             hCCeeeccceeeccccccCccccC-----CC--------------------------------------CccHH------
Confidence            999999999999999977651000     00                                      00000      


Q ss_pred             HHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCC
Q 005812          358 RKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDL  437 (676)
Q Consensus       358 ~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~  437 (676)
                       ..++                                                         .....+++||++||+..+
T Consensus       155 -eV~N---------------------------------------------------------Qssp~NtsVY~G~I~~~l  176 (321)
T KOG0148|consen  155 -EVYN---------------------------------------------------------QSSPDNTSVYVGNIASGL  176 (321)
T ss_pred             -HHhc---------------------------------------------------------cCCCCCceEEeCCcCccc
Confidence             0000                                                         022346899999999999


Q ss_pred             CHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCch
Q 005812          438 DNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       438 teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~  511 (676)
                      +|++|++.|+.||.|.+|+|+++      +|||||.|.+.|.|.+||..||     +..+.|+.+++.|.+...
T Consensus       177 te~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mN-----ntei~G~~VkCsWGKe~~  239 (321)
T KOG0148|consen  177 TEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMN-----NTEIGGQLVRCSWGKEGD  239 (321)
T ss_pred             cHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhc-----CceeCceEEEEeccccCC
Confidence            99999999999999999999977      7899999999999999999999     999999999999987654

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=100.00  E-value=6e-33  Score=291.40  Aligned_cols=370  Identities=20%  Similarity=0.294  Sum_probs=274.2

Q ss_pred             cceEEEEecCHHHHHHHHHHhCCceecCeEEEEeeccccchHH-----------Hhh--hhhchhhhhhhhhhccCCCCC
Q 005812           11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLE-----------QRR--SKVTQEVQAEDIEKTMDNKDG   77 (676)
Q Consensus        11 ~G~afV~F~~~edA~~Al~~~~g~~i~gr~i~v~~a~~k~~~~-----------~~~--~~~~~~~~~~~~~~~~~~~~~   77 (676)
                      +=||||.|..+++|.+|...++|+.+.||-|.|.++..+....           ..+  ...........|+..+++.+.
T Consensus       246 ~lfa~v~~~~~~~avka~~~~D~k~fqgrmlhvlp~~~k~~~~~~~~~~~~~~k~~ke~~rk~~~~~~~~wn~l~~~~~a  325 (725)
T KOG0110|consen  246 KLFAFVTFMFPEHAVKAYSELDGKVFQGRMLHVLPSKEKSTAKEDASELGSDYKKEKELKRKAASASFHSWNTLFMGANA  325 (725)
T ss_pred             HhhHHHhhhhhHHHHhhhhhccccccccceeeecCcchhhhhhhhHhhcCCcHHHHHHhccccchhcceecccccccccH
Confidence            3469999999999999999999999999999998886664332           111  111122344788888888888


Q ss_pred             cccccccccchhhcc---CCCCCC------------Cccccc-CcccCCCCccchhcccCcEEEEcCCCccccHHHHHHH
Q 005812           78 VISGAEKHSSKLLES---GKTVKP------------RKAATL-GIDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRL  141 (676)
Q Consensus        78 ~~~~~~~~~~~~~~~---~~~~~~------------r~~~~~-~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~  141 (676)
                      .....+.+++....-   ......            ...... ...-.+-...++..+...-++|+|||..+..++|..+
T Consensus       326 va~~~a~k~~v~k~~i~d~~~~gsavr~al~etr~~~e~~~~~ee~gV~l~~F~~~~rs~~vil~kNlpa~t~~~elt~~  405 (725)
T KOG0110|consen  326 VAGILAQKLGVEKSRILDGSLSGSAVRLALGETRVVQEVRRFFEENGVKLDAFSQAERSDTVILVKNLPAGTLSEELTEA  405 (725)
T ss_pred             HHHHHHHHhCCeeeeeechhhcchHHHHHHHHhhhchhhhhhHHhhCcccccchhhhhhcceeeeccCccccccHHHHHH
Confidence            776666554433310   000000            000000 0000000123446667789999999999999999999


Q ss_pred             hhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeEEEEecCCC------------
Q 005812          142 AGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGG------------  209 (676)
Q Consensus       142 F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~i~v~~~~~------------  209 (676)
                      |..||+|..+.+|            +.|.   .++|+|.++.+|.+|+..|.+..+...++++...+.            
T Consensus       406 F~~fG~i~rvllp------------~~G~---~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~dvf~~~pka~~~  470 (725)
T KOG0110|consen  406 FLRFGEIGRVLLP------------PGGT---GAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPEDVFTEDPKADDL  470 (725)
T ss_pred             hhcccccceeecC------------cccc---eeeeeecCccchHHHHHHhchhhhccCccccccChhhhccCCcccccc
Confidence            9999999999654            1233   289999999999999999988888777665421100            


Q ss_pred             --------------------------CC------------CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEccc
Q 005812          210 --------------------------EG------------SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHN  251 (676)
Q Consensus       210 --------------------------~~------------~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~  251 (676)
                                                ..            .....++|||+||+++++.++|..+|..+|.|.++.|...
T Consensus       471 ~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kk  550 (725)
T KOG0110|consen  471 SAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKK  550 (725)
T ss_pred             ccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEecc
Confidence                                      00            0112244999999999999999999999999999988775


Q ss_pred             CCC---CCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCc
Q 005812          252 TDT---GLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDD  328 (676)
Q Consensus       252 ~~~---~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  328 (676)
                      +..   -.+.|||||+|.++++|+.|++.|+|+.++|+.|.|.++..+..  ....   +                    
T Consensus       551 kd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~--~~~g---K--------------------  605 (725)
T KOG0110|consen  551 KDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPA--STVG---K--------------------  605 (725)
T ss_pred             ccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccc--cccc---c--------------------
Confidence            422   13559999999999999999999999999999999999862110  0000   0                    


Q ss_pred             ccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCC
Q 005812          329 AETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSS  408 (676)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  408 (676)
                                                                                                      
T Consensus       606 --------------------------------------------------------------------------------  605 (725)
T KOG0110|consen  606 --------------------------------------------------------------------------------  605 (725)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcC
Q 005812          409 KSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASK  488 (676)
Q Consensus       409 ~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~  488 (676)
                               ..........|.|+|||+.++..+|+++|..||.|.+|+|+.....+.++|||||+|-++.+|.+|+.+|.
T Consensus       606 ---------~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~  676 (725)
T KOG0110|consen  606 ---------KKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALG  676 (725)
T ss_pred             ---------ccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhc
Confidence                     00011124689999999999999999999999999999999876667789999999999999999999999


Q ss_pred             CCCCCCeeecCcEEEEEEccCchhhh
Q 005812          489 TTSGLGIFLKGRQLTVLKALDKKLAH  514 (676)
Q Consensus       489 ~~~~~g~~l~gr~l~v~~a~~k~~~~  514 (676)
                           .++|.||.|.+.||..-....
T Consensus       677 -----STHlyGRrLVLEwA~~d~~~e  697 (725)
T KOG0110|consen  677 -----STHLYGRRLVLEWAKSDNTME  697 (725)
T ss_pred             -----ccceechhhheehhccchHHH
Confidence                 999999999999998866533

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=100.00  E-value=2.8e-31  Score=296.12  Aligned_cols=307  Identities=19%  Similarity=0.208  Sum_probs=204.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccC------------CceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhC
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPV------------GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN  279 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~------------G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  279 (676)
                      .....++|||+|||+.+++++|+++|..+            +.|..+.+..      .+|||||+|.+.++|..||. |+
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~------~kg~afVeF~~~e~A~~Al~-l~  243 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINK------EKNFAFLEFRTVEEATFAMA-LD  243 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECC------CCCEEEEEeCCHHHHhhhhc-CC
Confidence            34456899999999999999999999874            3455555543      67999999999999999995 99


Q ss_pred             CceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHH
Q 005812          280 GQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARK  359 (676)
Q Consensus       280 ~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  359 (676)
                      |..|.|+.|.|........   .......   ......                             ...          
T Consensus       244 g~~~~g~~l~v~r~~~~~~---~~~~~~~---~~~~~~-----------------------------~~~----------  278 (509)
T TIGR01642       244 SIIYSNVFLKIRRPHDYIP---VPQITPE---VSQKNP-----------------------------DDN----------  278 (509)
T ss_pred             CeEeeCceeEecCccccCC---ccccCCC---CCCCCC-----------------------------ccc----------
Confidence            9999999999875422110   0000000   000000                             000          


Q ss_pred             HhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCH
Q 005812          360 VLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDN  439 (676)
Q Consensus       360 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te  439 (676)
                                 ..                            ...       .   ...........++|||+|||+.+++
T Consensus       279 -----------~~----------------------------~~~-------~---~~~~~~~~~~~~~l~v~nlp~~~~~  309 (509)
T TIGR01642       279 -----------AK----------------------------NVE-------K---LVNSTTVLDSKDRIYIGNLPLYLGE  309 (509)
T ss_pred             -----------cc----------------------------ccc-------c---ccccccCCCCCCEEEEeCCCCCCCH
Confidence                       00                            000       0   0000001123479999999999999


Q ss_pred             HHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhhhHhhh
Q 005812          440 EEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEID  519 (676)
Q Consensus       440 edl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~~~~~~  519 (676)
                      ++|+++|+.||.|..+.|+.+..+|.++|||||+|.+.++|..|+..||     |..|+|+.|.|.++..........  
T Consensus       310 ~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~-----g~~~~~~~l~v~~a~~~~~~~~~~--  382 (509)
T TIGR01642       310 DQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALN-----GKDTGDNKLHVQRACVGANQATID--  382 (509)
T ss_pred             HHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcC-----CCEECCeEEEEEECccCCCCCCcc--
Confidence            9999999999999999999998899999999999999999999999999     999999999999986532111000  


Q ss_pred             hhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCeEEEecCCcc--c--------
Q 005812          520 KSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKS--M--------  589 (676)
Q Consensus       520 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~V~nlp~~--~--------  589 (676)
                              ..+      +...... ....+.           .   ..+. . ...+..+|+|.||+..  +        
T Consensus       383 --------~~~------~~~~~~~-~~~~~~-----------~---~~~~-~-~~~~s~v~~l~N~~~~~~l~~d~~~~~  431 (509)
T TIGR01642       383 --------TSN------GMAPVTL-LAKALS-----------Q---SILQ-I-GGKPTKVVQLTNLVTGDDLMDDEEYEE  431 (509)
T ss_pred             --------ccc------ccccccc-ccccch-----------h---hhcc-c-cCCCceEEEeccCCchhHhcCcchHHH
Confidence                    000      0000000 000000           0   0000 0 0113468999999642  1        


Q ss_pred             CHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCCCCCcccCccc
Q 005812          590 TEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDA  669 (676)
Q Consensus       590 te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~~~~~~~~~~~  669 (676)
                      ..++|+++|.         +||.|.+|.|+++....   ..+.+.|+|||+|.++++|.+||..|||...  + .+.++|
T Consensus       432 ~~edl~~~f~---------~~G~v~~v~i~~~~~~~---~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~--~-gr~v~~  496 (509)
T TIGR01642       432 IYEDVKTEFS---------KYGPLINIVIPRPNGDR---NSTPGVGKVFLEYADVRSAEKAMEGMNGRKF--N-DRVVVA  496 (509)
T ss_pred             HHHHHHHHHH---------hcCCeeEEEeeccCcCC---CcCCCcceEEEEECCHHHHHHHHHHcCCCEE--C-CeEEEE
Confidence            2357788887         59999999998753211   1235679999999999999999999999742  2 355555


Q ss_pred             ccc
Q 005812          670 ADA  672 (676)
Q Consensus       670 ~~~  672 (676)
                      +|.
T Consensus       497 ~~~  499 (509)
T TIGR01642       497 AFY  499 (509)
T ss_pred             EEe
Confidence            553

Members of this subfamily are found in plants, metazoa and fungi.

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

Probab=100.00  E-value=2.4e-31  Score=263.26  Aligned_cols=173  Identities=27%  Similarity=0.408  Sum_probs=150.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCce-e--CCeeEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK-F--GKRPIA  289 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~-~--~g~~i~  289 (676)
                      ..+.-++||+-+|..|+|.||+.+|++||.|.+|.|++|+.++.++|||||.|.+.++|.+|+.+||+.. |  ..++|.
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvq  110 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQ  110 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCccee
Confidence            3456789999999999999999999999999999999999999999999999999999999999998865 4  347888


Q ss_pred             EEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCC
Q 005812          290 VDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTG  369 (676)
Q Consensus       290 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g  369 (676)
                      |.+++....                                                                       
T Consensus       111 vk~Ad~E~e-----------------------------------------------------------------------  119 (510)
T KOG0144|consen  111 VKYADGERE-----------------------------------------------------------------------  119 (510)
T ss_pred             ecccchhhh-----------------------------------------------------------------------
Confidence            888754321                                                                       


Q ss_pred             CCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhC
Q 005812          370 SLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAF  449 (676)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~  449 (676)
                                                                         .....+.|||+-|+..+||.||+++|++|
T Consensus       120 ---------------------------------------------------r~~~e~KLFvg~lsK~~te~evr~iFs~f  148 (510)
T KOG0144|consen  120 ---------------------------------------------------RIVEERKLFVGMLSKQCTENEVREIFSRF  148 (510)
T ss_pred             ---------------------------------------------------ccccchhhhhhhccccccHHHHHHHHHhh
Confidence                                                               00123689999999999999999999999


Q ss_pred             CceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc--EEEEEEccCchh
Q 005812          450 GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR--QLTVLKALDKKL  512 (676)
Q Consensus       450 G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr--~l~v~~a~~k~~  512 (676)
                      |.|++|+|++|. .+.++|||||+|.+.+-|..|++.||.    ...+.|+  +|.|.||.+++.
T Consensus       149 G~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng----~~tmeGcs~PLVVkFADtqkd  208 (510)
T KOG0144|consen  149 GHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNG----TQTMEGCSQPLVVKFADTQKD  208 (510)
T ss_pred             Cccchhhheecc-cccccceeEEEEehHHHHHHHHHhhcc----ceeeccCCCceEEEecccCCC
Confidence            999999999985 689999999999999999999999992    3556664  999999998663

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=1.4e-29  Score=236.58  Aligned_cols=163  Identities=26%  Similarity=0.422  Sum_probs=138.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      ..+||+.|...++-|+|++.|.+||.|..++|++|..+++++|||||.|-..++|++||..||     |..|++|.|+-.
T Consensus        63 fhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~Mn-----GqWlG~R~IRTN  137 (321)
T KOG0148|consen   63 FHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMN-----GQWLGRRTIRTN  137 (321)
T ss_pred             eeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhC-----Ceeeccceeecc
Confidence            479999999999999999999999999999999999999999999999999999999999999     999999999999


Q ss_pred             EccCchhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCeEEEecC
Q 005812          506 KALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNL  585 (676)
Q Consensus       506 ~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~V~nl  585 (676)
                      ||-.|.....                          +.+    ++          .++- -....|    ..|+|||.||
T Consensus       138 WATRKp~e~n--------------------------~~~----lt----------fdeV-~NQssp----~NtsVY~G~I  172 (321)
T KOG0148|consen  138 WATRKPSEMN--------------------------GKP----LT----------FDEV-YNQSSP----DNTSVYVGNI  172 (321)
T ss_pred             ccccCccccC--------------------------CCC----cc----------HHHH-hccCCC----CCceEEeCCc
Confidence            9987751110                          000    00          0000 001112    3488999999


Q ss_pred             CcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCC
Q 005812          586 PKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPS  659 (676)
Q Consensus       586 p~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~  659 (676)
                      +..+||++|++.|+         .||.|.+|++.++            +||+||.|.++|.|.+||-.+||...
T Consensus       173 ~~~lte~~mr~~Fs---------~fG~I~EVRvFk~------------qGYaFVrF~tkEaAahAIv~mNntei  225 (321)
T KOG0148|consen  173 ASGLTEDLMRQTFS---------PFGPIQEVRVFKD------------QGYAFVRFETKEAAAHAIVQMNNTEI  225 (321)
T ss_pred             CccccHHHHHHhcc---------cCCcceEEEEecc------------cceEEEEecchhhHHHHHHHhcCcee
Confidence            99999999999999         6999999999977            89999999999999999999998654

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.97  E-value=3e-29  Score=259.32  Aligned_cols=172  Identities=26%  Similarity=0.468  Sum_probs=156.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+++++++|+++|+.||.|.+|+|+.+..+++++|||||+|.++++|++|++.|++..+.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCC
Q 005812          292 WAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSL  371 (676)
Q Consensus       292 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  371 (676)
                      |+.+...                                                                         
T Consensus       183 ~a~p~~~-------------------------------------------------------------------------  189 (346)
T TIGR01659       183 YARPGGE-------------------------------------------------------------------------  189 (346)
T ss_pred             ccccccc-------------------------------------------------------------------------
Confidence            9865310                                                                         


Q ss_pred             CCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCc
Q 005812          372 PSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGE  451 (676)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~  451 (676)
                                                                        ....++|||.|||+.+++++|+++|++||.
T Consensus       190 --------------------------------------------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~  219 (346)
T TIGR01659       190 --------------------------------------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQ  219 (346)
T ss_pred             --------------------------------------------------ccccceeEEeCCCCcccHHHHHHHHHhcCC
Confidence                                                              001258999999999999999999999999


Q ss_pred             eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC--cEEEEEEccCch
Q 005812          452 VVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG--RQLTVLKALDKK  511 (676)
Q Consensus       452 v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g--r~l~v~~a~~k~  511 (676)
                      |..++|++++.++.++|||||+|.+.++|.+|++.||     +..+.|  ++|.|.++....
T Consensus       220 V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~ln-----g~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       220 IVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALN-----NVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             EEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhC-----CCccCCCceeEEEEECCccc
Confidence            9999999998899999999999999999999999999     888866  699999987653

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.96  E-value=1.9e-28  Score=253.32  Aligned_cols=170  Identities=18%  Similarity=0.248  Sum_probs=155.0

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeec
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIK  198 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~  198 (676)
                      ...++|||+|||+++++++|+++|+.||.|.+|+|+.++.         .++++|||||+|.++++|.+|++.||+..+.
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~---------tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~  175 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYK---------TGYSFGYAFVDFGSEADSQRAIKNLNGITVR  175 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC---------CCccCcEEEEEEccHHHHHHHHHHcCCCccC
Confidence            3567999999999999999999999999999999998764         4889999999999999999999999999999


Q ss_pred             CeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHh
Q 005812          199 GGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF  278 (676)
Q Consensus       199 ~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l  278 (676)
                      ++.|.|............++|||+|||..+++++|+++|++||.|..|.|++++.+++++|||||+|.+.++|++||+.|
T Consensus       176 gr~i~V~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~l  255 (346)
T TIGR01659       176 NKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISAL  255 (346)
T ss_pred             CceeeeecccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHh
Confidence            99999976544444456788999999999999999999999999999999999889999999999999999999999999


Q ss_pred             CCceeCC--eeEEEEEecCCC
Q 005812          279 NGQKFGK--RPIAVDWAVPKN  297 (676)
Q Consensus       279 ~~~~~~g--~~i~v~~a~~~~  297 (676)
                      |+..+.+  +.|.|.|+....
T Consensus       256 ng~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       256 NNVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             CCCccCCCceeEEEEECCccc
Confidence            9999865  789999987643

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.95  E-value=1.2e-26  Score=228.37  Aligned_cols=417  Identities=19%  Similarity=0.263  Sum_probs=270.4

Q ss_pred             cCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhC--CCee
Q 005812          120 VARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLH--QKEI  197 (676)
Q Consensus       120 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~--~~~~  197 (676)
                      .++-|.++|||++++|++|..++..||.|..+.+..             |++  .||++|.+.++|..-+....  -..+
T Consensus        27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lk-------------Gkn--QAflem~d~~sAvtmv~~y~~~~p~l   91 (492)
T KOG1190|consen   27 PSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLK-------------GKN--QAFLEMADEESAVTMVNYYTSVTPVL   91 (492)
T ss_pred             CcceeEeccCCccccHHHHHHhcccccceeeeeeec-------------cch--hhhhhhcchhhhhheeecccccCccc
Confidence            567899999999999999999999999999988542             333  69999999999988443221  1234


Q ss_pred             cCeEEEEecCC---------------------------------C-------CCCCCCCcEEEEcCCCCCCCHHHHHHhh
Q 005812          198 KGGTVWARQLG---------------------------------G-------EGSKTQKWKLIIRNIPFKAKVNEIKDMF  237 (676)
Q Consensus       198 ~~~~i~v~~~~---------------------------------~-------~~~~~~~~~v~V~nLp~~~~e~~l~~~F  237 (676)
                      .|.+|++....                                 .       ...+..--+++|.|+-+.++-+-|..+|
T Consensus        92 r~~~~yiq~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvF  171 (492)
T KOG1190|consen   92 RGQPIYIQYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVF  171 (492)
T ss_pred             cCcceeehhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHH
Confidence            45555543100                                 0       0111123467899999999999999999


Q ss_pred             ccCCceEEEEEcccCCCCCceeE-EEEEecCHHHHHHHHHHhCCcee--CCeeEEEEEecCCCCCCcCCcccCccCCCCC
Q 005812          238 SPVGLVWNVYIPHNTDTGLSKGF-AFVKFTCKRDAESAIQKFNGQKF--GKRPIAVDWAVPKNIYSSGGAAAGVQNKGDG  314 (676)
Q Consensus       238 ~~~G~i~~v~i~~~~~~~~~~g~-afV~f~~~~~A~~A~~~l~~~~~--~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~  314 (676)
                      ++||.|..|.-...     +.|| |+|+|.+.+.|+.|...|+|..|  +.+.|+|+|++-......-..      ....
T Consensus       172 S~fG~VlKIiTF~K-----nn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynn------dkSR  240 (492)
T KOG1190|consen  172 SKFGFVLKIITFTK-----NNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNN------DKSR  240 (492)
T ss_pred             hhcceeEEEEEEec-----ccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccc------cccc
Confidence            99999998766553     3343 99999999999999999999988  457888888865433221110      0000


Q ss_pred             CCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhc
Q 005812          315 NSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVN  394 (676)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~  394 (676)
                      +.+                       .-..|..+.    +..+...+...   .+..+...   +.+...+...      
T Consensus       241 DyT-----------------------np~LP~gd~----~p~l~~~~~aa---~~~~~~~~---g~p~aip~~~------  281 (492)
T KOG1190|consen  241 DYT-----------------------NPDLPVGDG----QPSLDQLMAAA---FGSVPAVH---GAPLAIPSGA------  281 (492)
T ss_pred             ccc-----------------------CCCCCCCcc----ccccchhhhcc---cccccccc---CCcccCCccc------
Confidence            000                       000000000    00000000000   00000000   0000000000      


Q ss_pred             cccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCC-CCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEE
Q 005812          395 ESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLP-FDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLK  473 (676)
Q Consensus       395 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp-~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~  473 (676)
                                 ........+...   .. .+..|.|.||. +.+|.+-|..+|+.||.|..|+|+.++     +--|+|.
T Consensus       282 -----------~~a~~a~~~~~~---~~-~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQ  341 (492)
T KOG1190|consen  282 -----------AGANAADGKIES---PS-ANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQ  341 (492)
T ss_pred             -----------hhhccccccccc---CC-CceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----Ccceeee
Confidence                       000000000000   00 14788888886 568999999999999999999999875     3469999


Q ss_pred             eCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhH
Q 005812          474 FKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDD  553 (676)
Q Consensus       474 F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~  553 (676)
                      |.+...|+-|+.+|+     |..|.|++|+|.+++                   ++++.+..+|+...+-...  +....
T Consensus       342 msd~~qAqLA~~hL~-----g~~l~gk~lrvt~SK-------------------H~~vqlp~egq~d~glT~d--y~~sp  395 (492)
T KOG1190|consen  342 MSDGQQAQLAMEHLE-----GHKLYGKKLRVTLSK-------------------HTNVQLPREGQEDQGLTKD--YGNSP  395 (492)
T ss_pred             ecchhHHHHHHHHhh-----cceecCceEEEeecc-------------------CccccCCCCCCcccccccc--CCCCc
Confidence            999999999999999     999999999999965                   3455556665544333221  11111


Q ss_pred             HHHHHHHHHHHhhcCCCCCccccCCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCc
Q 005812          554 MSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYS  633 (676)
Q Consensus       554 ~~~~~~~~~~~~~~~~~p~~~~~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s  633 (676)
                      +.     +..++...-..|...+..+|+..|+|.+++|++++++|.+        .-|.|+..++..           ..
T Consensus       396 Lh-----rfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~--------~g~~vkafkff~-----------kd  451 (492)
T KOG1190|consen  396 LH-----RFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQE--------PGGQVKAFKFFQ-----------KD  451 (492)
T ss_pred             hh-----hccCcccccccccCCchhheeeccCCcccchhHHHHhhhc--------CCceEEeeeecC-----------CC
Confidence            11     1112222222455556779999999999999999999996        455555555542           35


Q ss_pred             ceEEEEEeCChHHHHHHHHHHcCCCCCCCcccCccccc
Q 005812          634 RGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAAD  671 (676)
Q Consensus       634 ~g~afV~F~~~~~A~~Ai~~lng~~~~~~~~~~~~~~~  671 (676)
                      +-+|++.+.+.|+|..|+-.+++|.+--+.+.|...++
T Consensus       452 ~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSk  489 (492)
T KOG1190|consen  452 RKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSK  489 (492)
T ss_pred             cceeecccCChhHhhhhccccccccCCCCceEEEEeec
Confidence            77999999999999999999999998778888876554

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=5e-26  Score=220.33  Aligned_cols=179  Identities=27%  Similarity=0.489  Sum_probs=154.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      .|+|||+.+.+...|+.|+..|.+||+|.+|.+..|+.+++++|||||+|+-+|.|+.|++.|||..++||.|+|..  |
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr--P  190 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR--P  190 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC--C
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999973  2


Q ss_pred             CCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCC
Q 005812          296 KNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLS  375 (676)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  375 (676)
                      .+.....                                                 .-.+.++.....            
T Consensus       191 sNmpQAQ-------------------------------------------------piID~vqeeAk~------------  209 (544)
T KOG0124|consen  191 SNMPQAQ-------------------------------------------------PIIDMVQEEAKK------------  209 (544)
T ss_pred             CCCcccc-------------------------------------------------hHHHHHHHHHHh------------
Confidence            2211000                                                 001122211111            


Q ss_pred             CccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEE
Q 005812          376 DDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSF  455 (676)
Q Consensus       376 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v  455 (676)
                                                                       -++|||..+.++.+++||+..|+.||.|.+|
T Consensus       210 -------------------------------------------------fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C  240 (544)
T KOG0124|consen  210 -------------------------------------------------FNRIYVASVHPDLSETDIKSVFEAFGEIVKC  240 (544)
T ss_pred             -------------------------------------------------hheEEeeecCCCccHHHHHHHHHhhcceeeE
Confidence                                                             2589999999999999999999999999999


Q ss_pred             EEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCch
Q 005812          456 VPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       456 ~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~  511 (676)
                      .+-+++..+.++|||||+|.+..+-..|+..||     -+-|+|..|+|..+....
T Consensus       241 ~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMN-----lFDLGGQyLRVGk~vTPP  291 (544)
T KOG0124|consen  241 QLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN-----LFDLGGQYLRVGKCVTPP  291 (544)
T ss_pred             EeeccCCCCCccceeeEEeccccchHHHhhhcc-----hhhcccceEecccccCCC
Confidence            999998888899999999999999999999999     899999999999988755

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.94  E-value=8.4e-25  Score=216.62  Aligned_cols=243  Identities=16%  Similarity=0.155  Sum_probs=202.6

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhh-cCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCee
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAG-SIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEI  197 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~-~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~  197 (676)
                      ...|.+||+|||+++.+++|++||+ ..|+|+.|.+..|.          .|+++|+|.|+|.++|.+++|++.||...+
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~----------~GK~rGcavVEFk~~E~~qKa~E~lnk~~~  111 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE----------SGKARGCAVVEFKDPENVQKALEKLNKYEV  111 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc----------CCCcCCceEEEeeCHHHHHHHHHHhhhccc
Confidence            3456799999999999999999999 56899999998774          599999999999999999999999999999


Q ss_pred             cCeEEEEecCCCCC------CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHH
Q 005812          198 KGGTVWARQLGGEG------SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDA  271 (676)
Q Consensus       198 ~~~~i~v~~~~~~~------~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A  271 (676)
                      .|++|.|.......      ........|++++...+-..-|...|..-|...+-.+.+|. ++.+++..+++|++.-.+
T Consensus       112 ~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~-Dr~sr~~~t~t~~~~~~~  190 (608)
T KOG4212|consen  112 NGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDD-DRLSRRNNTNTMSNDYNN  190 (608)
T ss_pred             cCceEEEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccc-cccccccCcccccccccc
Confidence            99999997654322      12345789999999999999999999887877777777764 788999999999999888


Q ss_pred             HHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCch
Q 005812          272 ESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFD  351 (676)
Q Consensus       272 ~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  351 (676)
                      ..++..++.....-+.+++ +..|                                                        
T Consensus       191 ~~~~~lfgl~~~Flr~~h~-f~pP--------------------------------------------------------  213 (608)
T KOG4212|consen  191 SSNYNLFGLSASFLRSLHI-FSPP--------------------------------------------------------  213 (608)
T ss_pred             chhhhcccchhhhhhhccC-CCCC--------------------------------------------------------
Confidence            8888865554444444443 2211                                                        


Q ss_pred             hHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEc
Q 005812          352 EEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFIC  431 (676)
Q Consensus       352 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~  431 (676)
                                                                                              ....+||.
T Consensus       214 ------------------------------------------------------------------------l~~k~fva  221 (608)
T KOG4212|consen  214 ------------------------------------------------------------------------LHNKVFVA  221 (608)
T ss_pred             ------------------------------------------------------------------------ccceeeee
Confidence                                                                                    12479999


Q ss_pred             CCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEc
Q 005812          432 NLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA  507 (676)
Q Consensus       432 nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a  507 (676)
                      ||.+.+..+.|++.|.-.|.|.+|.+-.|+. |.++|+|.++|..+-+|..|+..++     +--+..++.++.+.
T Consensus       222 nl~~~vg~~kL~qvfgmAGkv~~vdf~idKe-G~s~G~~vi~y~hpveavqaIsml~-----~~g~~~~~~~~Rl~  291 (608)
T KOG4212|consen  222 NLDYKVGNKKLKQVFGMAGKVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAISMLD-----RQGLFDRRMTVRLD  291 (608)
T ss_pred             ccccccchHHHHHHhccceeeeeeceeeccc-cccCCeeEEEecchHHHHHHHHhhc-----cCCCccccceeecc
Confidence            9999999999999999999999998888875 6889999999999999999999998     76777777777663

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.93  E-value=2.3e-26  Score=236.05  Aligned_cols=325  Identities=21%  Similarity=0.311  Sum_probs=228.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++||+--|+...+..+|.++|+.+|.|..|+++.|..++.++|.|||+|.+.+....|+. |.|..+.|.+|.|....
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~sE  256 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLSE  256 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecccH
Confidence            35889999999999999999999999999999999999999999999999999999999996 89999999999998753


Q ss_pred             CCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCC
Q 005812          295 PKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSL  374 (676)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  374 (676)
                      ......                                                             .+.....+     
T Consensus       257 aeknr~-------------------------------------------------------------a~~s~a~~-----  270 (549)
T KOG0147|consen  257 AEKNRA-------------------------------------------------------------ANASPALQ-----  270 (549)
T ss_pred             HHHHHH-------------------------------------------------------------Hhcccccc-----
Confidence            322100                                                             00000000     


Q ss_pred             CCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE
Q 005812          375 SDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS  454 (676)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~  454 (676)
                            ..                                     ....+...|||+||.+.+++++|+.+|++||.|..
T Consensus       271 ------~k-------------------------------------~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~  307 (549)
T KOG0147|consen  271 ------GK-------------------------------------GFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIEN  307 (549)
T ss_pred             ------cc-------------------------------------ccccchhhhhhcccccCchHHHHhhhccCccccee
Confidence                  00                                     01112234999999999999999999999999999


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhhhHhhhhhcccccccCccccc
Q 005812          455 FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLA  534 (676)
Q Consensus       455 v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~  534 (676)
                      |.+++|..+|.++|||||+|...++|.+|+..||     |+.|.||.|.|.....+-...............+...+.+.
T Consensus       308 v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~ln-----gfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~  382 (549)
T KOG0147|consen  308 VQLTKDSETGRSKGFGFITFVNKEDARKALEQLN-----GFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLG  382 (549)
T ss_pred             eeeccccccccccCcceEEEecHHHHHHHHHHhc-----cceecCceEEEEEeeeecccccccccccccchhhccccccc
Confidence            9999998899999999999999999999999999     99999999999876654433222111100111112222111


Q ss_pred             ccCc--c----cCCCCCCCCCChhHHHH----HHHHHHHHh--hcCC-------CCCccccCCeEEEecC--CcccCHHH
Q 005812          535 KEGL--I----LEGTPAAEGVSDDDMSK----RQMLHEKKM--TKLQ-------SPNFHVSRTRLVIYNL--PKSMTEKG  593 (676)
Q Consensus       535 ~~g~--~----~~~~~~~~~~~~~~~~~----~~~~~~~~~--~~~~-------~p~~~~~~~~l~V~nl--p~~~te~~  593 (676)
                      ..|.  .    .++.. -+..+...-..    .........  -...       .|.+.++..|+.++|+  |...|+..
T Consensus       383 ~~g~~Ql~~kla~~~~-~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n  461 (549)
T KOG0147|consen  383 SGGRNQLMAKLAEGKG-RSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPN  461 (549)
T ss_pred             cccHHHHHHHHhccCC-ccccchhhhHHHhccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcc
Confidence            1110  0    00000 00000000000    000000000  0001       2334467789999999  99999999


Q ss_pred             HHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCCCCCcccCcccc
Q 005812          594 LKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAA  670 (676)
Q Consensus       594 l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~~~~~~~~~~~~  670 (676)
                      |..-+.+.|..+|. +||.|..|.+-.           .|.|+.||.|.+.+.|..|+.+|||.   |+..+-+-++
T Consensus       462 ~d~eI~edV~Eec~-k~g~v~hi~vd~-----------ns~g~VYvrc~s~~~A~~a~~alhgr---WF~gr~Ita~  523 (549)
T KOG0147|consen  462 WDQEIREDVIEECG-KHGKVCHIFVDK-----------NSAGCVYVRCPSAEAAGTAVKALHGR---WFAGRMITAK  523 (549)
T ss_pred             hhhHHHHHHHHHHH-hcCCeeEEEEcc-----------CCCceEEEecCcHHHHHHHHHHHhhh---hhccceeEEE
Confidence            99999999999997 699997776643           34599999999999999999999996   6654444333

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.93  E-value=3.5e-25  Score=227.35  Aligned_cols=330  Identities=22%  Similarity=0.309  Sum_probs=222.5

Q ss_pred             chhcccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCC
Q 005812          115 SQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQ  194 (676)
Q Consensus       115 ~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~  194 (676)
                      +-..+..++||+..|+...+..+|.++|+.+|.|..|+++.|+.         .++++|.|||+|.+.+....|+. |.|
T Consensus       173 ~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~---------s~rskgi~Yvef~D~~sVp~aia-LsG  242 (549)
T KOG0147|consen  173 SPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRN---------SRRSKGIAYVEFCDEQSVPLAIA-LSG  242 (549)
T ss_pred             CchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeecccc---------chhhcceeEEEEecccchhhHhh-hcC
Confidence            44557889999999999999999999999999999999999874         47899999999999999999996 999


Q ss_pred             CeecCeEEEEecCCC--------------CCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeE
Q 005812          195 KEIKGGTVWARQLGG--------------EGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGF  260 (676)
Q Consensus       195 ~~~~~~~i~v~~~~~--------------~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~  260 (676)
                      ..+.|-+|.|.....              .....+...|||+||..++++++|+.+|++||.|..|.++++.++|.++||
T Consensus       243 qrllg~pv~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgf  322 (549)
T KOG0147|consen  243 QRLLGVPVIVQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGF  322 (549)
T ss_pred             CcccCceeEecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCc
Confidence            999999998864221              111223334999999999999999999999999999999999999999999


Q ss_pred             EEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCcc
Q 005812          261 AFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSE  340 (676)
Q Consensus       261 afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (676)
                      |||+|.+.++|++|+..|||..|.|+.|+|.....+-......     ...    .+  .+++    +-.+.        
T Consensus       323 Gfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~-----~~~----~d--~D~~----d~~gl--------  379 (549)
T KOG0147|consen  323 GFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVDTKEAA-----VTQ----FD--FDED----DRQGL--------  379 (549)
T ss_pred             ceEEEecHHHHHHHHHHhccceecCceEEEEEeeeeccccccc-----ccc----cc--cchh----hcccc--------
Confidence            9999999999999999999999999999998765432111000     000    00  0000    00000        


Q ss_pred             ccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccC
Q 005812          341 KEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEG  420 (676)
Q Consensus       341 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  420 (676)
                         ......   ..+...+... ...  -.+++.......-..  ...      ......++.+  .....|...  .+.
T Consensus       380 ---~~~~~g---~~Ql~~kla~-~~~--~~~~s~~~~~l~~~~--~~~------~~~~~~~~~~--~~~~~p~~~--~p~  438 (549)
T KOG0147|consen  380 ---SLGSGG---RNQLMAKLAE-GKG--RSLPSTAISALLLLA--KLA------SAAQFNGVVR--VRSVDPADA--SPA  438 (549)
T ss_pred             ---cccccc---HHHHHHHHhc-cCC--ccccchhhhHHHhcc--ccc------hHHhhcCCcC--ccccCcccc--ccc
Confidence               000000   1111111111 110  011111100000000  000      0000000000  000000100  111


Q ss_pred             CCCCCCeEEEcCC--CCCCC--------HHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCC
Q 005812          421 EDELQNTIFICNL--PFDLD--------NEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTT  490 (676)
Q Consensus       421 ~~~~~~~l~V~nL--p~~~t--------eedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~  490 (676)
                      -..++.++.|+||  |...|        .+||.+-+.+||.|..|.+  |+   .+-|+.||.|.+.+.|..|+.+||  
T Consensus       439 ~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~v--d~---ns~g~VYvrc~s~~~A~~a~~alh--  511 (549)
T KOG0147|consen  439 FDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFV--DK---NSAGCVYVRCPSAEAAGTAVKALH--  511 (549)
T ss_pred             cCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEE--cc---CCCceEEEecCcHHHHHHHHHHHh--
Confidence            2256678999998  22222        5789999999999998765  32   234999999999999999999999  


Q ss_pred             CCCCeeecCcEEEEEEcc
Q 005812          491 SGLGIFLKGRQLTVLKAL  508 (676)
Q Consensus       491 ~~~g~~l~gr~l~v~~a~  508 (676)
                         |.+|.|+.|.+.|-.
T Consensus       512 ---grWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  512 ---GRWFAGRMITAKYLP  526 (549)
T ss_pred             ---hhhhccceeEEEEee
Confidence               999999999999843

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.92  E-value=4.1e-25  Score=195.26  Aligned_cols=173  Identities=30%  Similarity=0.447  Sum_probs=156.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      ......+|||+||+..++++.|+++|-+.|+|.++.+++++.+...+|||||+|.++++|+-|++-||...+-|++|+|.
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVN   84 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCC
Q 005812          292 WAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSL  371 (676)
Q Consensus       292 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  371 (676)
                      .+.....                                                                         
T Consensus        85 kas~~~~-------------------------------------------------------------------------   91 (203)
T KOG0131|consen   85 KASAHQK-------------------------------------------------------------------------   91 (203)
T ss_pred             ecccccc-------------------------------------------------------------------------
Confidence            8742110                                                                         


Q ss_pred             CCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCc
Q 005812          372 PSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGE  451 (676)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~  451 (676)
                                                                       ....+.+|||+||.+.+++.-|.+.|+.||.
T Consensus        92 -------------------------------------------------nl~vganlfvgNLd~~vDe~~L~dtFsafG~  122 (203)
T KOG0131|consen   92 -------------------------------------------------NLDVGANLFVGNLDPEVDEKLLYDTFSAFGV  122 (203)
T ss_pred             -------------------------------------------------cccccccccccccCcchhHHHHHHHHHhccc
Confidence                                                             0111368999999999999999999999998


Q ss_pred             eeEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCch
Q 005812          452 VVSF-VPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       452 v~~v-~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~  511 (676)
                      +... .|+++..+|.++|||||.|.+.+.+.+|+..||     |..+..|+++|.++..++
T Consensus       123 l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~n-----gq~l~nr~itv~ya~k~~  178 (203)
T KOG0131|consen  123 LISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMN-----GQYLCNRPITVSYAFKKD  178 (203)
T ss_pred             cccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhc-----cchhcCCceEEEEEEecC
Confidence            8763 789999999999999999999999999999999     999999999999998764

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.92  E-value=5.5e-24  Score=206.21  Aligned_cols=166  Identities=14%  Similarity=0.213  Sum_probs=149.7

Q ss_pred             cCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecC
Q 005812          120 VARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKG  199 (676)
Q Consensus       120 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~  199 (676)
                      .-++||||.|.+..-|+.|+..|..||+|.++.+.-|..         .++.+|||||+|+-+|.|+.|++.|||..++|
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~---------T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGG  182 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPA---------TGKHKGFAFVEYEVPEAAQLALEQMNGQMLGG  182 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccc---------cccccceEEEEEeCcHHHHHHHHHhccccccC
Confidence            467899999999999999999999999999999776654         38999999999999999999999999999999


Q ss_pred             eEEEEecCCCCCC-----------CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCH
Q 005812          200 GTVWARQLGGEGS-----------KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK  268 (676)
Q Consensus       200 ~~i~v~~~~~~~~-----------~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~  268 (676)
                      +.|.|-..+.-..           ...-.+|||..+.++.+++||+..|+-||.|..|.+-+.+..+.++||+||+|.+.
T Consensus       183 RNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~  262 (544)
T KOG0124|consen  183 RNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNL  262 (544)
T ss_pred             ccccccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccc
Confidence            9999864433221           12357999999999999999999999999999999999998889999999999999


Q ss_pred             HHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          269 RDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       269 ~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      .+-..|+..||-..++|.-++|-.+.
T Consensus       263 qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  263 QSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             cchHHHhhhcchhhcccceEeccccc
Confidence            99999999999999999999997653

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.91  E-value=1.3e-21  Score=190.71  Aligned_cols=427  Identities=18%  Similarity=0.242  Sum_probs=268.5

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHh--CCCe
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALL--HQKE  196 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l--~~~~  196 (676)
                      ..+-.|.|.+|-..+++.+|.+..+.||+|.-|.++..               +..|.|+|++.+.|+.++...  +...
T Consensus        29 ~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~---------------~r~alvefedi~~akn~Vnfaa~n~i~   93 (494)
T KOG1456|consen   29 NPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH---------------KRQALVEFEDIEGAKNCVNFAADNQIY   93 (494)
T ss_pred             CCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc---------------cceeeeeeccccchhhheehhccCccc
Confidence            34557999999999999999999999999999987643               234999999999999997633  2223


Q ss_pred             ecCeEEEE--------ecCCCCCCCCCCcEEEEcCC--CCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEec
Q 005812          197 IKGGTVWA--------RQLGGEGSKTQKWKLIIRNI--PFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFT  266 (676)
Q Consensus       197 ~~~~~i~v--------~~~~~~~~~~~~~~v~V~nL--p~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~  266 (676)
                      +.|.....        ++. +......+..|.+.=|  -+.+|.+-|..++...|.|.+|.|++.  +|   -.|.|+|.
T Consensus        94 i~gq~Al~NyStsq~i~R~-g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ng---VQAmVEFd  167 (494)
T KOG1456|consen   94 IAGQQALFNYSTSQCIERP-GDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NG---VQAMVEFD  167 (494)
T ss_pred             ccCchhhcccchhhhhccC-CCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cc---eeeEEeec
Confidence            33332211        111 2334455666766655  456899999999999999999999875  33   45999999


Q ss_pred             CHHHHHHHHHHhCCcee--CCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCC-ccccC
Q 005812          267 CKRDAESAIQKFNGQKF--GKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNS-SEKED  343 (676)
Q Consensus       267 ~~~~A~~A~~~l~~~~~--~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~  343 (676)
                      +.+.|++|...|||..|  +.++|+|+|++|..+...+...+              .++-.-.+..+..+.... .....
T Consensus       168 sv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~D--------------twDyTlp~~~~~~~~g~~~~~r~~  233 (494)
T KOG1456|consen  168 SVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKD--------------TWDYTLPDLRGPYDPGRNHYDRQR  233 (494)
T ss_pred             hhHHHHHHHhhcccccccccceeEEEEecCcceeeeeecCCc--------------cccccCCCCCCCCCCCCCCCcccc
Confidence            99999999999999987  56899999999876533221110              011111111111110000 00000


Q ss_pred             CCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccc-cccCCCCCCCchhhccccccccccc-cCCCCCCCCCCCcccCC
Q 005812          344 LPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSA-LVKGNKEQDSDKTVNESAKVSDVSK-LNSSKSKPKSLKQTEGE  421 (676)
Q Consensus       344 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  421 (676)
                      .+....+                    .++   ... .-.++.....       ....+..| .................
T Consensus       234 ~p~~~~~--------------------~ps---s~~G~h~~y~sg~~-------~~p~~~~P~r~~~~~~~~~g~a~p~g  283 (494)
T KOG1456|consen  234 QPAPLGY--------------------HPS---SRGGGHSGYYSGDR-------HGPPHPPPSRYRDGYRDGRGYASPGG  283 (494)
T ss_pred             CCCccCC--------------------Chh---hcCCCCCCCccccc-------CCCCCCCCCCCccccccCCCCCCCCC
Confidence            0000000                    000   000 0000000000       00000000 00000000001111245


Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          422 DELQNTIFICNLPF-DLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       422 ~~~~~~l~V~nLp~-~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ..+++.+.|.+|.. ..+-+.|.++|..||.|..|++|+-+     .|.|.|++.+..+.++|+..||     +..+.|.
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLn-----n~~lfG~  353 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLN-----NIPLFGG  353 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhc-----cCccccc
Confidence            56789999999986 56889999999999999999998764     6889999999999999999999     9999999


Q ss_pred             EEEEEEccCchhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCeE
Q 005812          501 QLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRL  580 (676)
Q Consensus       501 ~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l  580 (676)
                      +|.|.+++..--              ..-+.++..+     ++|...+++.+.-.+.....+..+.+++.|     +++|
T Consensus       354 kl~v~~SkQ~~v--------------~~~~pflLpD-----gSpSfKdys~SkNnRFssp~qAsKNrIq~P-----s~vL  409 (494)
T KOG1456|consen  354 KLNVCVSKQNFV--------------SPVQPFLLPD-----GSPSFKDYSGSKNNRFSSPEQASKNRIQPP-----SNVL  409 (494)
T ss_pred             eEEEeecccccc--------------ccCCceecCC-----CCcchhhcccccccccCChhHhhcccccCC-----ccee
Confidence            999987543211              1112333333     333333333222222222223333344444     4789


Q ss_pred             EEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCCC
Q 005812          581 VIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSK  660 (676)
Q Consensus       581 ~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~~  660 (676)
                      +..|.|..+||+.|.++|.+-        --.-.+|++..-+.        .....|.+||++.++|..||..||.+|..
T Consensus       410 HffNaP~~vtEe~l~~i~nek--------~v~~~svkvFp~ks--------erSssGllEfe~~s~Aveal~~~NH~pi~  473 (494)
T KOG1456|consen  410 HFFNAPLGVTEEQLIGICNEK--------DVPPTSVKVFPLKS--------ERSSSGLLEFENKSDAVEALMKLNHYPIE  473 (494)
T ss_pred             EEecCCCccCHHHHHHHhhhc--------CCCcceEEeecccc--------cccccceeeeehHHHHHHHHHHhcccccc
Confidence            999999999999999999952        11234566664432        33468899999999999999999999883

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.90  E-value=1e-23  Score=186.52  Aligned_cols=168  Identities=22%  Similarity=0.317  Sum_probs=152.2

Q ss_pred             CcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCe
Q 005812          121 ARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGG  200 (676)
Q Consensus       121 ~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~  200 (676)
                      ..+|||+||+..++++-|+++|-++|+|..+++|.|+.+         ...+|||||+|.++|+|.-|++-||...|.|+
T Consensus         9 d~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~---------~~~qGygF~Ef~~eedadYAikiln~VkLYgr   79 (203)
T KOG0131|consen    9 DATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVT---------QKHQGYGFAEFRTEEDADYAIKILNMVKLYGR   79 (203)
T ss_pred             CceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhc---------ccccceeEEEEechhhhHHHHHHHHHHHhcCc
Confidence            458999999999999999999999999999999998864         46799999999999999999999999999999


Q ss_pred             EEEEecCCCC-CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEE-EEEcccCCCCCceeEEEEEecCHHHHHHHHHHh
Q 005812          201 TVWARQLGGE-GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWN-VYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF  278 (676)
Q Consensus       201 ~i~v~~~~~~-~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~-v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l  278 (676)
                      +|++...+.. .....+..+||+||.+.++|..|...|+.||.|.. -.|++++.+|.++|||||.|.+.+.+.+|+..+
T Consensus        80 pIrv~kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~  159 (203)
T KOG0131|consen   80 PIRVNKASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSM  159 (203)
T ss_pred             eeEEEecccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHh
Confidence            9999876522 23344589999999999999999999999999875 488899999999999999999999999999999


Q ss_pred             CCceeCCeeEEEEEecCCC
Q 005812          279 NGQKFGKRPIAVDWAVPKN  297 (676)
Q Consensus       279 ~~~~~~g~~i~v~~a~~~~  297 (676)
                      ||..+++++|.|.++..+.
T Consensus       160 ngq~l~nr~itv~ya~k~~  178 (203)
T KOG0131|consen  160 NGQYLCNRPITVSYAFKKD  178 (203)
T ss_pred             ccchhcCCceEEEEEEecC
Confidence            9999999999999996554

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.89  E-value=6.9e-21  Score=193.33  Aligned_cols=455  Identities=15%  Similarity=0.154  Sum_probs=252.8

Q ss_pred             cCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecC
Q 005812          120 VARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKG  199 (676)
Q Consensus       120 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~  199 (676)
                      ...-|.+.+|||++|++||+++|+.|+ |+.+.++           +.+|+..|-|||+|.+.+++++|++ .+...+..
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~-----------r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~   75 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIP-----------RRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGH   75 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEe-----------ccCCCcCcceEEEeechHHHHHHHH-hhHHHhCC
Confidence            445688999999999999999999995 6666654           2459999999999999999999998 57777777


Q ss_pred             eEEEEecC-----------CCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEE-EEEcccCCCCCceeEEEEEecC
Q 005812          200 GTVWARQL-----------GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWN-VYIPHNTDTGLSKGFAFVKFTC  267 (676)
Q Consensus       200 ~~i~v~~~-----------~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~-v~i~~~~~~~~~~g~afV~f~~  267 (676)
                      +.|.|-..           .+.........|-+++||+.++++||.++|+..-.+.. +.++.++ .+++.|-|||+|++
T Consensus        76 RYIEVf~~~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~s  154 (510)
T KOG4211|consen   76 RYIEVFTAGGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFES  154 (510)
T ss_pred             ceEEEEccCCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecC
Confidence            77766322           12223346789999999999999999999998766665 4455554 67799999999999


Q ss_pred             HHHHHHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCC
Q 005812          268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSN  347 (676)
Q Consensus       268 ~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  347 (676)
                      .+.|++||.. |...|..+-|.|..+..................     ..+.+..     .....-.+     -.....
T Consensus       155 qe~ae~Al~r-hre~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~r-----pGpy~~~-----~a~Rg~~d-----~~~~~~  218 (510)
T KOG4211|consen  155 QESAEIALGR-HRENIGHRYIEVFRSSRAEVKRAAGPGDGRVGR-----PGPYDRP-----GAPRGGYD-----YGQGRD  218 (510)
T ss_pred             HHHHHHHHHH-HHHhhccceEEeehhHHHHHHhhccccccccCC-----CCccccc-----cCCccccc-----cccccC
Confidence            9999999997 888899999999866433221111100000000     0000000     00000000     000000


Q ss_pred             CCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCe
Q 005812          348 ADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNT  427 (676)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  427 (676)
                      .....        ...-....+.+ ...........+     ........+...... .+.............-...+..
T Consensus       219 ~~~~~--------~r~g~~~~g~~-g~~~~~~~~d~~-----~~gs~~~~~~~~~~~-~~g~~~~g~~g~~~~~~~~g~f  283 (510)
T KOG4211|consen  219 PGRNA--------TRYGAGGEGYY-GFSRYPSLQDYG-----NFGSYGGGRDPNYPV-SSGPHRQGGAGDYGNGGPGGHF  283 (510)
T ss_pred             CCccc--------cccccccCCcc-ccccCccccccc-----cccccccccccccCC-CCCcccCCCcccccCCCCCCce
Confidence            00000        00000000000 000000000000     000000000000000 0000000000011112223378


Q ss_pred             EEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEc
Q 005812          428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA  507 (676)
Q Consensus       428 l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a  507 (676)
                      ++.++||+..++.+|.++|+..-.+ .|.|-.. .+|+.+|-|+|+|.|.++|..|+.. +     +..+..|.|.+..-
T Consensus       284 v~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig-~dGr~TGEAdveF~t~edav~Amsk-d-----~anm~hrYVElFln  355 (510)
T KOG4211|consen  284 VHMRGLPYDATENDIANFFSPLNPY-RVHIEIG-PDGRATGEADVEFATGEDAVGAMGK-D-----GANMGHRYVELFLN  355 (510)
T ss_pred             eeecCCCccCCCcchhhhcCCCCce-eEEEEeC-CCCccCCcceeecccchhhHhhhcc-C-----CcccCcceeeeccc
Confidence            9999999999999999999986444 5555444 5789999999999999999999965 3     67888888877653


Q ss_pred             cCchhhhhHhhhhhcccccccCccccc-----ccCcccCCCCCCCC-----C--ChhHHHHHHHHHHHHhhcCCCCC---
Q 005812          508 LDKKLAHDKEIDKSKNETNDHRNLYLA-----KEGLILEGTPAAEG-----V--SDDDMSKRQMLHEKKMTKLQSPN---  572 (676)
Q Consensus       508 ~~k~~~~~~~~~~~~~~~~~~~~~~~~-----~~g~~~~~~~~~~~-----~--~~~~~~~~~~~~~~~~~~~~~p~---  572 (676)
                      -... +..-        ..........     ..+...+..+...+     .  ++..+.. ..-...-......|.   
T Consensus       356 ~~~g-a~g~--------~~~s~~~g~~~~~~~~~~Gg~a~g~~~gG~~g~~~~~~~~G~~~-~~~~~~~~~Gy~g~~~~~  425 (510)
T KOG4211|consen  356 GAPG-ASGG--------GGPSGPGGVGSSGDRNGGGGYASGSYGGGGNGGGGRGSPYGRPS-DGYSSPGGGGYSGPRGYG  425 (510)
T ss_pred             CCcc-cccC--------ccCCCCCCccccccccCCCCccccccccCCCCCccccCCCCCCc-ccccCCCCCCCcCcccCC
Confidence            2111 0000        0000000000     00000000000000     0  0000000 000000000000000   


Q ss_pred             --ccccCCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHH
Q 005812          573 --FHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVA  650 (676)
Q Consensus       573 --~~~~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~A  650 (676)
                        .....-+|..+.+|+..++.++.++|..         ++.- +|.|.+|+.-       ...|.|-|.|.+.++++.|
T Consensus       426 ~~~~~e~~~~~~rgap~~a~eadv~d~~~~---------~~~a-~~~~~yd~~~-------~~~~~a~~~~~~~~~~q~a  488 (510)
T KOG4211|consen  426 RGPQNEHFVIRMRGAPFRASEADVYDFFHP---------IRPA-QVELLYDHQF-------QRSGDARVIFYNRKDYQDA  488 (510)
T ss_pred             CCccccccccCcCCCCccccccchhhcccc---------cCcc-cccccccccc-------cccCceeEEEechhhhHHH
Confidence              0001146889999999999999999994         5543 4888888653       3489999999999999999


Q ss_pred             HHHH
Q 005812          651 LRVL  654 (676)
Q Consensus       651 i~~l  654 (676)
                      |..=
T Consensus       489 ~~~~  492 (510)
T KOG4211|consen  489 LMKD  492 (510)
T ss_pred             HHhh
Confidence            8754

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.88  E-value=4.2e-22  Score=185.71  Aligned_cols=299  Identities=20%  Similarity=0.245  Sum_probs=176.4

Q ss_pred             eEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhC
Q 005812          200 GTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN  279 (676)
Q Consensus       200 ~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  279 (676)
                      +.|.|++...+....+.++|||+.|...-.|+|++.+|..||.|.+|.+.+.+ +|.++|+|||.|.+..+|+.||..||
T Consensus         3 rpiqvkpadsesrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLH   81 (371)
T KOG0146|consen    3 RPIQVKPADSESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALH   81 (371)
T ss_pred             CCccccccccccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhc
Confidence            45666665555556678999999999999999999999999999999999875 78899999999999999999999999


Q ss_pred             Ccee-C--CeeEEEEEecCCCCCCcCCc-cc----CccCCCCCCCCCCCCCCCCCCcccccCC---CCCCccccCCCCCC
Q 005812          280 GQKF-G--KRPIAVDWAVPKNIYSSGGA-AA----GVQNKGDGNSDSGSDDDLGDDDAETASD---DSNSSEKEDLPSNA  348 (676)
Q Consensus       280 ~~~~-~--g~~i~v~~a~~~~~~~~~~~-~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~  348 (676)
                      |..- -  ...|.|.+++..+....+.. ..    +.-+........        -..-.+..   .+..-.....+-..
T Consensus        82 gSqTmpGASSSLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~--------~~ay~qalmQqQa~~~at~~~~~L~  153 (371)
T KOG0146|consen   82 GSQTMPGASSSLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGA--------YGAYAQALMQQQAALLATVAGPYLS  153 (371)
T ss_pred             ccccCCCCccceEEEeccchHHHHHHHHHHHHHHhcccCccccccch--------hHHHHHHHHHHHHHHHHhhcccccC
Confidence            9864 3  46788999865432211100 00    000000000000        00000000   00000000000000


Q ss_pred             CchhH----HHHH-HHHhhccc-----ccCCCCCCC------CC---ccccccCCCCCCCchhh---ccccccc------
Q 005812          349 DFDEE----VDIA-RKVLNKLT-----STTGSLPSL------SD---DSALVKGNKEQDSDKTV---NESAKVS------  400 (676)
Q Consensus       349 ~~~~~----~~~~-~~~~~~~~-----~~~g~~~~~------~~---~~~~~~~~~~~~~~~~~---~~~~~~~------  400 (676)
                      .....    .+.. .-..+.+.     ...|...+.      ..   ......|+.........   ......+      
T Consensus       154 p~~~~~~~~mQ~~aA~~angl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pyp  233 (371)
T KOG0146|consen  154 PMAAFAAAQMQQMAALNANGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYP  233 (371)
T ss_pred             hhhhhHHHHHHHHHHHhhcccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCC
Confidence            00000    0000 00000000     000000000      00   00000111111000000   0000000      


Q ss_pred             --------------------------cccccCCCCCC-CCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCcee
Q 005812          401 --------------------------DVSKLNSSKSK-PKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVV  453 (676)
Q Consensus       401 --------------------------~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~  453 (676)
                                                .+.+....-.. +.......+..+.+|+|||.+||.+..+.||.++|-.||.|.
T Consensus       234 aQsp~va~~lq~a~~g~~~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhiv  313 (371)
T KOG0146|consen  234 AQSPTVADPLQQAYAGVQQYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIV  313 (371)
T ss_pred             CCCccccchhhhhhhhHHHHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhcccccee
Confidence                                      00111111111 111122346788899999999999999999999999999999


Q ss_pred             EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchh
Q 005812          454 SFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKL  512 (676)
Q Consensus       454 ~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~  512 (676)
                      +.+++.|..++.+++|+||.|+++.+|+.||.+||     |+.|+-++|+|.+.++|+.
T Consensus       314 SaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMN-----GFQIGMKRLKVQLKRPkda  367 (371)
T KOG0146|consen  314 SAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMN-----GFQIGMKRLKVQLKRPKDA  367 (371)
T ss_pred             eeeeeehhccccccceeeEecCCchhHHHHHHHhc-----chhhhhhhhhhhhcCcccc
Confidence            99999999999999999999999999999999999     9999999999999888763

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.88  E-value=6.2e-21  Score=189.34  Aligned_cols=213  Identities=20%  Similarity=0.184  Sum_probs=170.4

Q ss_pred             cCCCCcccceEEEEecCHHHHHHHHHHhCCceecCeEEEEeeccccchHHHhhhhhchhhhhhhhhhccCCCCCcccccc
Q 005812            4 KKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAEDIEKTMDNKDGVISGAE   83 (676)
Q Consensus         4 ~~~tg~s~G~afV~F~~~edA~~Al~~~~g~~i~gr~i~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (676)
                      -...|++||+|.|+|+++|.+++|++.||...+.||.|.|+--...    ++ .                          
T Consensus        79 ~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d~----q~-~--------------------------  127 (608)
T KOG4212|consen   79 FDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHDE----QR-D--------------------------  127 (608)
T ss_pred             cccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCch----hh-h--------------------------
Confidence            3578999999999999999999999999999999999999543110    00 0                          


Q ss_pred             cccchhhccCCCCCCCcccccCcccCCCCccchhcccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhc
Q 005812           84 KHSSKLLESGKTVKPRKAATLGIDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQH  163 (676)
Q Consensus        84 ~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~  163 (676)
                                                   ......+.+-+.|++++....-..-|...|.--|.+..-....|       
T Consensus       128 -----------------------------~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D-------  171 (608)
T KOG4212|consen  128 -----------------------------QYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRD-------  171 (608)
T ss_pred             -----------------------------hhhheeeccCcccccCcceecccccccccCCCCccccCCCCccc-------
Confidence                                         01122355668999999999989999999988887666655544       


Q ss_pred             ccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCce
Q 005812          164 GLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLV  243 (676)
Q Consensus       164 ~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i  243 (676)
                         .++.+++..++.|.+.-.+..++..++......+.+..      -.++....+||.||.+.+....|.+.|.-.|.|
T Consensus       172 ---~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~Flr~~h~------f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv  242 (608)
T KOG4212|consen  172 ---DDRLSRRNNTNTMSNDYNNSSNYNLFGLSASFLRSLHI------FSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKV  242 (608)
T ss_pred             ---ccccccccCccccccccccchhhhcccchhhhhhhccC------CCCCccceeeeeccccccchHHHHHHhccceee
Confidence               35788999999999999888888766655444444433      134455689999999999999999999999999


Q ss_pred             EEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          244 WNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       244 ~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ..+.+-.+++ |.++|||.++|..+-+|-.|+..|++.-+..++..+...
T Consensus       243 ~~vdf~idKe-G~s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~Rl~  291 (608)
T KOG4212|consen  243 QSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVRLD  291 (608)
T ss_pred             eeeceeeccc-cccCCeeEEEecchHHHHHHHHhhccCCCccccceeecc
Confidence            9999888874 579999999999999999999999987777777777653

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.86  E-value=4.3e-20  Score=182.44  Aligned_cols=272  Identities=19%  Similarity=0.194  Sum_probs=199.3

Q ss_pred             cEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccce-EEEEeCCHHHHHHHHHHhCCCeecCe
Q 005812          122 RTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDA-SAVLYTTVKSACASVALLHQKEIKGG  200 (676)
Q Consensus       122 ~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~-afV~F~~~~~A~~A~~~l~~~~~~~~  200 (676)
                      -+++|.|+-+.++-+-|+.+|+.||.|..+.-.              .++.+| |.|+|.+.+.|+.|...|+|..|...
T Consensus       151 Lr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF--------------~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyng  216 (492)
T KOG1190|consen  151 LRTIIENMFYPVSLDVLHQVFSKFGFVLKIITF--------------TKNNGFQALVQYTDAVSAQAAKLALDGQNIYNG  216 (492)
T ss_pred             EEEEeccceeeeEHHHHHHHHhhcceeEEEEEE--------------ecccchhhhhhccchhhHHHHHHhccCCcccCc
Confidence            468999999999999999999999999998743              345555 89999999999999999999999887


Q ss_pred             EEEEec-------------------C------CC-----------------------C---------------CCCC--C
Q 005812          201 TVWARQ-------------------L------GG-----------------------E---------------GSKT--Q  215 (676)
Q Consensus       201 ~i~v~~-------------------~------~~-----------------------~---------------~~~~--~  215 (676)
                      ++.+|-                   .      .+                       +               ....  .
T Consensus       217 cCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~  296 (492)
T KOG1190|consen  217 CCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSA  296 (492)
T ss_pred             eeEEEeehhhcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCC
Confidence            665430                   0      00                       0               0001  1


Q ss_pred             CcEEEEcCCCC-CCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          216 KWKLIIRNIPF-KAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       216 ~~~v~V~nLp~-~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      +..|.|.||.. .+|.+-|..+|.-||.|.+|+|..++.     --|+|+|.+...|+-|++.|+|..+.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            57899999966 589999999999999999999998743     459999999999999999999999999999999997


Q ss_pred             CCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCC
Q 005812          295 PKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSL  374 (676)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  374 (676)
                      ......+....          .+                         ...+.+.                   +..+-+
T Consensus       372 H~~vqlp~egq----------~d-------------------------~glT~dy-------------------~~spLh  397 (492)
T KOG1190|consen  372 HTNVQLPREGQ----------ED-------------------------QGLTKDY-------------------GNSPLH  397 (492)
T ss_pred             CccccCCCCCC----------cc-------------------------ccccccC-------------------CCCchh
Confidence            76542221100          00                         0000000                   000000


Q ss_pred             CCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE
Q 005812          375 SDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS  454 (676)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~  454 (676)
                      ..                     +..+             .+-...--+++.+|++.|+|..++||+|+++|..-|-..+
T Consensus       398 rf---------------------kkpg-------------sKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vk  443 (492)
T KOG1190|consen  398 RF---------------------KKPG-------------SKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVK  443 (492)
T ss_pred             hc---------------------cCcc-------------cccccccCCchhheeeccCCcccchhHHHHhhhcCCceEE
Confidence            00                     0000             0000001234679999999999999999999999887766


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc-EEEEEEccC
Q 005812          455 FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR-QLTVLKALD  509 (676)
Q Consensus       455 v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr-~l~v~~a~~  509 (676)
                      ...+    -++.+.+|++.+.+.++|..|+-.++     ...+++. .|+|+|+++
T Consensus       444 afkf----f~kd~kmal~q~~sveeA~~ali~~h-----nh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  444 AFKF----FQKDRKMALPQLESVEEAIQALIDLH-----NHYLGENHHLRVSFSKS  490 (492)
T ss_pred             eeee----cCCCcceeecccCChhHhhhhccccc-----cccCCCCceEEEEeecc
Confidence            5332    23457799999999999999999999     7888755 999999764

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.85  E-value=2e-21  Score=183.87  Aligned_cols=148  Identities=21%  Similarity=0.271  Sum_probs=137.1

Q ss_pred             EEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeEE
Q 005812          123 TVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTV  202 (676)
Q Consensus       123 ~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~i  202 (676)
                      .|||+|||..+++.+|+.+|++||.|.+|.|+                 +.||||+.++...|..|+.+||+..|+|..|
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv-----------------KNYgFVHiEdktaaedairNLhgYtLhg~nI   66 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIV-----------------KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNI   66 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeee-----------------cccceEEeecccccHHHHhhcccceecceEE
Confidence            58999999999999999999999999999987                 5689999999999999999999999999999


Q ss_pred             EEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCce
Q 005812          203 WARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK  282 (676)
Q Consensus       203 ~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~  282 (676)
                      .|......  .....+|+|+||.+.++..+|+..|.+||+|.+|.|++        +|+||.|...++|..|++.|+++.
T Consensus        67 nVeaSksK--sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--------dy~fvh~d~~eda~~air~l~~~~  136 (346)
T KOG0109|consen   67 NVEASKSK--SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--------DYAFVHFDRAEDAVEAIRGLDNTE  136 (346)
T ss_pred             EEEecccc--CCCccccccCCCCccccCHHHhhhhcccCCceeeeeec--------ceeEEEEeeccchHHHHhcccccc
Confidence            99765432  44568999999999999999999999999999999987        589999999999999999999999


Q ss_pred             eCCeeEEEEEecCCC
Q 005812          283 FGKRPIAVDWAVPKN  297 (676)
Q Consensus       283 ~~g~~i~v~~a~~~~  297 (676)
                      |.|++++|..+..+-
T Consensus       137 ~~gk~m~vq~stsrl  151 (346)
T KOG0109|consen  137 FQGKRMHVQLSTSRL  151 (346)
T ss_pred             cccceeeeeeecccc
Confidence            999999999987654

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.85  E-value=3.4e-20  Score=188.28  Aligned_cols=300  Identities=20%  Similarity=0.248  Sum_probs=191.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      .....|-+++|||.+|++||+++|+.++ |.++.+++.  +|+..|-|||+|.+++++++|+++ +...+..+-|.|-.+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR--NGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc--CCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEcc
Confidence            3456788999999999999999999986 888777764  799999999999999999999995 888899999999877


Q ss_pred             cCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCC
Q 005812          294 VPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPS  373 (676)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  373 (676)
                      .+....-                                                               .+...+.   
T Consensus        84 ~~~e~d~---------------------------------------------------------------~~~~~g~---   97 (510)
T KOG4211|consen   84 GGAEADW---------------------------------------------------------------VMRPGGP---   97 (510)
T ss_pred             CCccccc---------------------------------------------------------------cccCCCC---
Confidence            5432100                                                               0000000   


Q ss_pred             CCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCcee
Q 005812          374 LSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVV  453 (676)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~  453 (676)
                                                                    ........|.+++||+.||++||.+||+..-.|.
T Consensus        98 ----------------------------------------------~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~  131 (510)
T KOG4211|consen   98 ----------------------------------------------NSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVP  131 (510)
T ss_pred             ----------------------------------------------CCCCCCceEEecCCCccCcHHHHHHHhcCCcccc
Confidence                                                          0001235899999999999999999999875555


Q ss_pred             E-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhhhHhhhhhcccc-------
Q 005812          454 S-FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNET-------  525 (676)
Q Consensus       454 ~-v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~~~~~~~~~~~~-------  525 (676)
                      . +.++++ ..+++.|-|||+|.+.+.|+.|+...      ...|+-|.|.|..+...+...-..........       
T Consensus       132 ~gi~l~~d-~rgR~tGEAfVqF~sqe~ae~Al~rh------re~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~  204 (510)
T KOG4211|consen  132 DGILLPMD-QRGRPTGEAFVQFESQESAEIALGRH------RENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRP  204 (510)
T ss_pred             cceeeecc-CCCCcccceEEEecCHHHHHHHHHHH------HHhhccceEEeehhHHHHHHhhccccccccCCCCccccc
Confidence            5 334444 46789999999999999999999875      48889999999886543322111000000000       


Q ss_pred             cccCccccccc--Cccc---------------CCCCCC---CCCChhHHHHHHHHHHH-HhhcCCC----CCccccCCeE
Q 005812          526 NDHRNLYLAKE--GLIL---------------EGTPAA---EGVSDDDMSKRQMLHEK-KMTKLQS----PNFHVSRTRL  580 (676)
Q Consensus       526 ~~~~~~~~~~~--g~~~---------------~~~~~~---~~~~~~~~~~~~~~~~~-~~~~~~~----p~~~~~~~~l  580 (676)
                      ...+..+.-..  +...               ...+..   ................. -.+....    -+.......+
T Consensus       205 ~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv  284 (510)
T KOG4211|consen  205 GAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFV  284 (510)
T ss_pred             cCCccccccccccCCCccccccccccCCccccccCccccccccccccccccccccCCCCCcccCCCcccccCCCCCCcee
Confidence            00000000000  0000               000000   00000000000000000 0001111    1111122679


Q ss_pred             EEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHH
Q 005812          581 VIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRV  653 (676)
Q Consensus       581 ~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~  653 (676)
                      +.++||+..++.++.++|+          ......|+|-..+       .++..|.|+|+|.|+++|..||-.
T Consensus       285 ~MRGlpy~a~~~di~nfFs----------pl~p~~v~i~ig~-------dGr~TGEAdveF~t~edav~Amsk  340 (510)
T KOG4211|consen  285 HMRGLPYDATENDIANFFS----------PLNPYRVHIEIGP-------DGRATGEADVEFATGEDAVGAMGK  340 (510)
T ss_pred             eecCCCccCCCcchhhhcC----------CCCceeEEEEeCC-------CCccCCcceeecccchhhHhhhcc
Confidence            9999999999999999999          4444467776654       268899999999999999999853

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.84  E-value=6.6e-21  Score=180.40  Aligned_cols=149  Identities=26%  Similarity=0.409  Sum_probs=137.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      ..|||+|||..+++.+|+.+|++||.|.+|.|+++        ||||..++...|+.|++.|||..|.|..|.|+-++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            36999999999999999999999999999999874        7999999999999999999999999999999988665


Q ss_pred             CCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCC
Q 005812          297 NIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSD  376 (676)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  376 (676)
                      ..                                                                              
T Consensus        75 sk------------------------------------------------------------------------------   76 (346)
T KOG0109|consen   75 SK------------------------------------------------------------------------------   76 (346)
T ss_pred             CC------------------------------------------------------------------------------
Confidence            21                                                                              


Q ss_pred             ccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEE
Q 005812          377 DSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFV  456 (676)
Q Consensus       377 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~  456 (676)
                                                                     .+.+|+|+||.+.++.+||+..|++||+|.+|.
T Consensus        77 -----------------------------------------------~stkl~vgNis~tctn~ElRa~fe~ygpviecd  109 (346)
T KOG0109|consen   77 -----------------------------------------------ASTKLHVGNISPTCTNQELRAKFEKYGPVIECD  109 (346)
T ss_pred             -----------------------------------------------CccccccCCCCccccCHHHhhhhcccCCceeee
Confidence                                                           136899999999999999999999999999999


Q ss_pred             EeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCch
Q 005812          457 PVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       457 i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~  511 (676)
                      |+        ++|+||.|+-.++|..|++.|+     +..|.|++++|+.+-++-
T Consensus       110 iv--------kdy~fvh~d~~eda~~air~l~-----~~~~~gk~m~vq~stsrl  151 (346)
T KOG0109|consen  110 IV--------KDYAFVHFDRAEDAVEAIRGLD-----NTEFQGKRMHVQLSTSRL  151 (346)
T ss_pred             ee--------cceeEEEEeeccchHHHHhccc-----ccccccceeeeeeecccc
Confidence            87        4599999999999999999999     999999999999987654

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.76  E-value=2e-18  Score=172.92  Aligned_cols=176  Identities=25%  Similarity=0.457  Sum_probs=154.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++|||++|++.++++.|+.+|..||.|.+|.+++++.+++++||+||+|.+++...++|.. ....|.|+.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            678999999999999999999999999999999999999999999999999999999999984 6777999999999887


Q ss_pred             CCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCC
Q 005812          295 PKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSL  374 (676)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  374 (676)
                      ++.......                                                                       
T Consensus        84 ~r~~~~~~~-----------------------------------------------------------------------   92 (311)
T KOG4205|consen   84 SREDQTKVG-----------------------------------------------------------------------   92 (311)
T ss_pred             Ccccccccc-----------------------------------------------------------------------
Confidence            764311000                                                                       


Q ss_pred             CCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE
Q 005812          375 SDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS  454 (676)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~  454 (676)
                                                                    .......|||++||.++++++++++|.+||.|..
T Consensus        93 ----------------------------------------------~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~  126 (311)
T KOG4205|consen   93 ----------------------------------------------RHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVAD  126 (311)
T ss_pred             ----------------------------------------------cccceeEEEecCcCCCCchHHHhhhhhccceeEe
Confidence                                                          0002468999999999999999999999999999


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhh
Q 005812          455 FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAH  514 (676)
Q Consensus       455 v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~  514 (676)
                      +.++.|..+.+++||+||.|.+.+.+.+++.. .     -..|.|+.+.|..|.+++...
T Consensus       127 ~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~-~-----f~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  127 VVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQ-K-----FHDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             eEEeecccccccccceeeEeccccccceeccc-c-----eeeecCceeeEeeccchhhcc
Confidence            99999999999999999999999999888754 4     689999999999999986443

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.75  E-value=3.8e-18  Score=159.49  Aligned_cols=169  Identities=24%  Similarity=0.358  Sum_probs=144.9

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCe-e
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKE-I  197 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~-~  197 (676)
                      ...|.|||+-|...-.|+|++.+|..||.|.+|.+..-          .+|.++|+|||.|.+.-+|..|+..|+|.. +
T Consensus        17 ~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg----------~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTm   86 (371)
T KOG0146|consen   17 GDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRG----------PDGNSKGCAFVKFSSHAEAQAAINALHGSQTM   86 (371)
T ss_pred             ccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecC----------CCCCCCCceEEEeccchHHHHHHHHhcccccC
Confidence            35678999999999999999999999999999998754          469999999999999999999999999853 2


Q ss_pred             cCe--EEEEe----------------------------------------------------------------------
Q 005812          198 KGG--TVWAR----------------------------------------------------------------------  205 (676)
Q Consensus       198 ~~~--~i~v~----------------------------------------------------------------------  205 (676)
                      .|-  .+-|+                                                                      
T Consensus        87 pGASSSLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~  166 (371)
T KOG0146|consen   87 PGASSSLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQM  166 (371)
T ss_pred             CCCccceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHH
Confidence            232  11110                                                                      


Q ss_pred             --------------c--------------------------------------------------CC-------------
Q 005812          206 --------------Q--------------------------------------------------LG-------------  208 (676)
Q Consensus       206 --------------~--------------------------------------------------~~-------------  208 (676)
                                    +                                                  +.             
T Consensus       167 aA~~angl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a  246 (371)
T KOG0146|consen  167 AALNANGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQA  246 (371)
T ss_pred             HHHhhcccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhh
Confidence                          0                                                  00             


Q ss_pred             -------------------------------CCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCc
Q 005812          209 -------------------------------GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLS  257 (676)
Q Consensus       209 -------------------------------~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~  257 (676)
                                                     ......+.|.|||-.||....+.+|...|-+||.|.+.++..|+.++.+
T Consensus       247 ~~g~~~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQS  326 (371)
T KOG0146|consen  247 YAGVQQYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQS  326 (371)
T ss_pred             hhhHHHHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccc
Confidence                                           0011346799999999999999999999999999999999999999999


Q ss_pred             eeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCC
Q 005812          258 KGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKN  297 (676)
Q Consensus       258 ~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~  297 (676)
                      ++|+||.|.++.+|+.||..|||..|+-++|+|.+..|++
T Consensus       327 KCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkd  366 (371)
T KOG0146|consen  327 KCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKD  366 (371)
T ss_pred             cceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCccc
Confidence            9999999999999999999999999999999999887775

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.74  E-value=4.4e-18  Score=170.46  Aligned_cols=170  Identities=19%  Similarity=0.310  Sum_probs=147.6

Q ss_pred             cCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecC
Q 005812          120 VARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKG  199 (676)
Q Consensus       120 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~  199 (676)
                      ..+.|||++|+|+++++.|++.|.+||+|.+|.++.|+.         .++++||+||.|.+++....++. .....|.|
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~---------t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dg   74 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPS---------TGRSRGFGFVTFATPEGVDAVLN-ARTHKLDG   74 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCC---------CCCcccccceecCCCcchheeec-ccccccCC
Confidence            456899999999999999999999999999999999875         39999999999999999999877 34556777


Q ss_pred             eEEEEecCCCCC------CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHH
Q 005812          200 GTVWARQLGGEG------SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAES  273 (676)
Q Consensus       200 ~~i~v~~~~~~~------~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~  273 (676)
                      +.|.+...-...      .......|||++||.++++++++++|.+||.|..+.++.|..+.+++||+||.|.+++.+.+
T Consensus        75 r~ve~k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdk  154 (311)
T KOG4205|consen   75 RSVEPKRAVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDK  154 (311)
T ss_pred             ccccceeccCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccce
Confidence            777654322111      12235699999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCceeCCeeEEEEEecCCCCCC
Q 005812          274 AIQKFNGQKFGKRPIAVDWAVPKNIYS  300 (676)
Q Consensus       274 A~~~l~~~~~~g~~i~v~~a~~~~~~~  300 (676)
                      ++.. ..+.|.|+.+.|..|.|+....
T Consensus       155 v~~~-~f~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  155 VTLQ-KFHDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             eccc-ceeeecCceeeEeeccchhhcc
Confidence            9994 8899999999999999987544

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.74  E-value=7.8e-16  Score=150.61  Aligned_cols=328  Identities=14%  Similarity=0.154  Sum_probs=222.2

Q ss_pred             ccceEEEEecCHHHHHHHHHH--hCCceecCeEEEEeeccccchHHHhhhhhchhhhhhhhhhccCCCCCcccccccccc
Q 005812           10 HRGFGYVQFAVMEDANRAVEM--KNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAEDIEKTMDNKDGVISGAEKHSS   87 (676)
Q Consensus        10 s~G~afV~F~~~edA~~Al~~--~~g~~i~gr~i~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (676)
                      .+..|.|+|++.+.|.+++..  -+...+.|+.-.+.+++++.-                                    
T Consensus        66 ~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NyStsq~i------------------------------------  109 (494)
T KOG1456|consen   66 HKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYSTSQCI------------------------------------  109 (494)
T ss_pred             ccceeeeeeccccchhhheehhccCcccccCchhhcccchhhhh------------------------------------
Confidence            456899999999999999876  344467777777766643310                                    


Q ss_pred             hhhccCCCCCCCcccccCcccCCCCccchhcccCcEEE--EcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhccc
Q 005812           88 KLLESGKTVKPRKAATLGIDLADKEDCSQKQRVARTVI--IGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGL  165 (676)
Q Consensus        88 ~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~l~--V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~  165 (676)
                                .|+.       .+..      ..+..|.  |-|--+.+|.+-|+.+...+|.|..|.|+.          
T Consensus       110 ----------~R~g-------~es~------~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfk----------  156 (494)
T KOG1456|consen  110 ----------ERPG-------DESA------TPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFK----------  156 (494)
T ss_pred             ----------ccCC-------CCCC------CCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEe----------
Confidence                      0000       0000      1122333  445556899999999999999999999873          


Q ss_pred             ccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeEEEEe------------c---------------------------
Q 005812          166 AQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWAR------------Q---------------------------  206 (676)
Q Consensus       166 ~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~i~v~------------~---------------------------  206 (676)
                          ++-=.|.|+|++.+.|++|.+.|||..|....+.+.            .                           
T Consensus       157 ----kngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~  232 (494)
T KOG1456|consen  157 ----KNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQ  232 (494)
T ss_pred             ----ccceeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccc
Confidence                222349999999999999999999999886644321            0                           


Q ss_pred             -C-----------C---------------------------------CCCCCCCCcEEEEcCCCCC-CCHHHHHHhhccC
Q 005812          207 -L-----------G---------------------------------GEGSKTQKWKLIIRNIPFK-AKVNEIKDMFSPV  240 (676)
Q Consensus       207 -~-----------~---------------------------------~~~~~~~~~~v~V~nLp~~-~~e~~l~~~F~~~  240 (676)
                       .           .                                 .+....+.+.++|-+|... ++-+.|..+|-.|
T Consensus       233 ~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClY  312 (494)
T KOG1456|consen  233 RQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLY  312 (494)
T ss_pred             cCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhc
Confidence             0           0                                 0011234688999999875 7789999999999


Q ss_pred             CceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCC
Q 005812          241 GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGS  320 (676)
Q Consensus       241 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  320 (676)
                      |.|++|++++.     ..|-|.|++.+..+.++|+..||+..+.|.+|.|.+++..-....  +              ..
T Consensus       313 GNV~rvkFmkT-----k~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~--~--------------pf  371 (494)
T KOG1456|consen  313 GNVERVKFMKT-----KPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPV--Q--------------PF  371 (494)
T ss_pred             CceeeEEEeec-----ccceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccccccC--C--------------ce
Confidence            99999999986     347799999999999999999999999999999998854322110  0              00


Q ss_pred             CCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccc
Q 005812          321 DDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVS  400 (676)
Q Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  400 (676)
                      ..++.....+.          =..+.+..|.+..++.+                                          
T Consensus       372 lLpDgSpSfKd----------ys~SkNnRFssp~qAsK------------------------------------------  399 (494)
T KOG1456|consen  372 LLPDGSPSFKD----------YSGSKNNRFSSPEQASK------------------------------------------  399 (494)
T ss_pred             ecCCCCcchhh----------cccccccccCChhHhhc------------------------------------------
Confidence            00000000000          00111122222211111                                          


Q ss_pred             cccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCc-eeEEEEeecCCCCCcceEEEEEeCCHHH
Q 005812          401 DVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGE-VVSFVPVLHQVTKRPKGTGFLKFKTVEA  479 (676)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~-v~~v~i~~~~~~~~~~g~afV~F~t~~~  479 (676)
                                        .+-..++++|+.-|.|..+||+.|..+|...+. -.+|+|+.-+ +.+ ...+.++|++.++
T Consensus       400 ------------------NrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp~k-ser-SssGllEfe~~s~  459 (494)
T KOG1456|consen  400 ------------------NRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPLK-SER-SSSGLLEFENKSD  459 (494)
T ss_pred             ------------------ccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeeccc-ccc-cccceeeeehHHH
Confidence                              112345689999999999999999999997653 4566776554 332 4568899999999


Q ss_pred             HHHHHHHcCCCCCCCeeecCc----EEEEEEcc
Q 005812          480 ATAAVSASKTTSGLGIFLKGR----QLTVLKAL  508 (676)
Q Consensus       480 A~~Al~~l~~~~~~g~~l~gr----~l~v~~a~  508 (676)
                      |..||..+|     ...+.+.    +..+.|+.
T Consensus       460 Aveal~~~N-----H~pi~~p~gs~PfilKlcf  487 (494)
T KOG1456|consen  460 AVEALMKLN-----HYPIEGPNGSFPFILKLCF  487 (494)
T ss_pred             HHHHHHHhc-----cccccCCCCCCCeeeeeee
Confidence            999999999     8888753    44444443

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.71  E-value=7e-16  Score=143.06  Aligned_cols=209  Identities=21%  Similarity=0.282  Sum_probs=148.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHH----hhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEE
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKD----MFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIA  289 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~----~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~  289 (676)
                      .++.+|||.||+..+..++|+.    +|++||.|.+|...+   +.+.+|-|||.|.+.+.|..|+..|+|..|-|+.++
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            3445999999999999999888    999999999988876   567899999999999999999999999999999999


Q ss_pred             EEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCC
Q 005812          290 VDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTG  369 (676)
Q Consensus       290 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g  369 (676)
                      |+||..+.+........-..+.......+.          .....        ....+..+                   
T Consensus        84 iqyA~s~sdii~~~~~~~v~~~~k~~~~~~----------~~~~~--------~~~~ng~~-------------------  126 (221)
T KOG4206|consen   84 IQYAKSDSDIIAQAPGTFVEKEKKINGEIL----------ARIKQ--------PLDTNGHF-------------------  126 (221)
T ss_pred             eecccCccchhhccCceeccccCccccccc----------cccCC--------cccccccc-------------------
Confidence            999987765443322110000000000000          00000        00000000                   


Q ss_pred             CCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhC
Q 005812          370 SLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAF  449 (676)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~  449 (676)
                                                         .+...+..+.+.. .....++..||+.|||..++.+.+..+|.+|
T Consensus       127 -----------------------------------~~~~~~~~p~p~~-~~~~ppn~ilf~~niP~es~~e~l~~lf~qf  170 (221)
T KOG4206|consen  127 -----------------------------------YNMNRMNLPPPFL-AQMAPPNNILFLTNIPSESESEMLSDLFEQF  170 (221)
T ss_pred             -----------------------------------cccccccCCCCcc-ccCCCCceEEEEecCCcchhHHHHHHHHhhC
Confidence                                               0000000011111 2245567899999999999999999999999


Q ss_pred             CceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec-CcEEEEEEcc
Q 005812          450 GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK-GRQLTVLKAL  508 (676)
Q Consensus       450 G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~-gr~l~v~~a~  508 (676)
                      .....++++..     ..+.|||+|.+...|..|...+.     ++.+- .+.+.|.++.
T Consensus       171 ~g~keir~i~~-----~~~iAfve~~~d~~a~~a~~~lq-----~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  171 PGFKEIRLIPP-----RSGIAFVEFLSDRQASAAQQALQ-----GFKITKKNTMQITFAK  220 (221)
T ss_pred             cccceeEeccC-----CCceeEEecchhhhhHHHhhhhc-----cceeccCceEEecccC
Confidence            99999987654     37899999999999999999999     88887 8888888764

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.70  E-value=1.2e-16  Score=167.51  Aligned_cols=301  Identities=20%  Similarity=0.316  Sum_probs=205.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccC-----------Cc-eEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCC
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPV-----------GL-VWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG  280 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~-----------G~-i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~  280 (676)
                      ......++|+++|..++++....+|..-           |+ +..+.+..      .+.|||++|.+.++|..|+. +++
T Consensus       172 t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~------~~nfa~ie~~s~~~at~~~~-~~~  244 (500)
T KOG0120|consen  172 TRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNL------EKNFAFIEFRSISEATEAMA-LDG  244 (500)
T ss_pred             hhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecc------cccceeEEecCCCchhhhhc-ccc
Confidence            3456899999999999999999998753           22 55555544      56799999999999999998 689


Q ss_pred             ceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHH
Q 005812          281 QKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKV  360 (676)
Q Consensus       281 ~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  360 (676)
                      ..+.|..+++..-............                                                       
T Consensus       245 ~~f~g~~~~~~r~~d~~~~p~~~~~-------------------------------------------------------  269 (500)
T KOG0120|consen  245 IIFEGRPLKIRRPHDYQPVPGITLS-------------------------------------------------------  269 (500)
T ss_pred             hhhCCCCceecccccccCCccchhh-------------------------------------------------------
Confidence            9999998887532211100000000                                                       


Q ss_pred             hhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHH
Q 005812          361 LNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNE  440 (676)
Q Consensus       361 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~tee  440 (676)
                          ....+...   ....                                      ........+.+||.+||..+++.
T Consensus       270 ----~~~~~~~~---~~~~--------------------------------------~t~~~~~~~ki~v~~lp~~l~~~  304 (500)
T KOG0120|consen  270 ----PSQLGKVG---LLPA--------------------------------------STDVPDSPNKIFVGGLPLYLTED  304 (500)
T ss_pred             ----hccccccC---Cccc--------------------------------------ccCcccccchhhhccCcCccCHH
Confidence                00000000   0000                                      00011224689999999999999


Q ss_pred             HHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhhhHhhhh
Q 005812          441 EVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDK  520 (676)
Q Consensus       441 dl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~~~~~~~  520 (676)
                      .++++...||.+....++.+..+|.++||||.+|-++.....|++.||     |..++++.|.|..|..-.....     
T Consensus       305 q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLn-----Gm~lgd~~lvvq~A~~g~~~~~-----  374 (500)
T KOG0120|consen  305 QVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLN-----GMQLGDKKLVVQRAIVGASNAN-----  374 (500)
T ss_pred             HHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccc-----hhhhcCceeEeehhhccchhcc-----
Confidence            999999999999999999999999999999999999999999999999     9999999999999875321110     


Q ss_pred             hcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCeEEEecC--CcccCHHHHHHHH
Q 005812          521 SKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNL--PKSMTEKGLKKLC  598 (676)
Q Consensus       521 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~V~nl--p~~~te~~l~~~F  598 (676)
                            .+.++.  . .+ ..+.                      ..+.-+....+...|.+.|+  |..+..++-.+-+
T Consensus       375 ------~~~~~~--~-~~-~~~i----------------------~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeI  422 (500)
T KOG0120|consen  375 ------VNFNIS--Q-SQ-VPGI----------------------PLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEI  422 (500)
T ss_pred             ------ccCCcc--c-cc-cccc----------------------hhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHH
Confidence                  000000  0 00 0000                      00000111224456777777  5555554444445


Q ss_pred             HHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCCCCCcccCcccc
Q 005812          599 IDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAA  670 (676)
Q Consensus       599 ~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~~~~~~~~~~~~  670 (676)
                      -+.|+-+|. .||.|.+|.|+++....   ......|-.||+|.+.++|++|+.+|+|.  .|+  .|.+|+
T Consensus       423 lEdvr~ec~-k~g~v~~v~ipr~~~~~---~~~~G~GkVFVefas~ed~qrA~~~L~Gr--KF~--nRtVvt  486 (500)
T KOG0120|consen  423 LEDVRTECA-KFGAVRSVEIPRPYPDE---NPVPGTGKVFVEFADTEDSQRAMEELTGR--KFA--NRTVVA  486 (500)
T ss_pred             HHHHHHHhc-ccCceeEEecCCCCCCC---CcCCCcccEEEEecChHHHHHHHHHccCc--eeC--CcEEEE
Confidence            556777787 59999999999883221   22355788899999999999999999998  343  566654

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.70  E-value=1e-16  Score=168.18  Aligned_cols=274  Identities=20%  Similarity=0.265  Sum_probs=205.2

Q ss_pred             chhcccCcEEEEcCCCccccHHHHHHHhhcC-----------C-CeEEEEeeCCchhhhhcccccCCCccceEEEEeCCH
Q 005812          115 SQKQRVARTVIIGGLLNADMAEEVHRLAGSI-----------G-TVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTV  182 (676)
Q Consensus       115 ~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~-----------G-~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~  182 (676)
                      ......++.++|+++|..+.++.+..+|..-           | .+..+.+               .....+||++|.+.
T Consensus       169 ~~~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~---------------n~~~nfa~ie~~s~  233 (500)
T KOG0120|consen  169 SQATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQL---------------NLEKNFAFIEFRSI  233 (500)
T ss_pred             cchhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeee---------------cccccceeEEecCC
Confidence            4455678899999999999999999998854           2 2444442               34567899999999


Q ss_pred             HHHHHHHHHhCCCeecCeEEEEecCCC-----------------------CCCCCCCcEEEEcCCCCCCCHHHHHHhhcc
Q 005812          183 KSACASVALLHQKEIKGGTVWARQLGG-----------------------EGSKTQKWKLIIRNIPFKAKVNEIKDMFSP  239 (676)
Q Consensus       183 ~~A~~A~~~l~~~~~~~~~i~v~~~~~-----------------------~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~  239 (676)
                      ++|..|+. +++..+.|..+.+.....                       .......+.+||++||...++.++.++...
T Consensus       234 ~~at~~~~-~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~  312 (500)
T KOG0120|consen  234 SEATEAMA-LDGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDS  312 (500)
T ss_pred             Cchhhhhc-ccchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHh
Confidence            99999987 788888888776643211                       112334689999999999999999999999


Q ss_pred             CCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCC
Q 005812          240 VGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSG  319 (676)
Q Consensus       240 ~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  319 (676)
                      ||.+....++.+..+|.++||||.+|.++.-...|+..|||..+++..|.|..+.+..........         ..+  
T Consensus       313 fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~---------~~~--  381 (500)
T KOG0120|consen  313 FGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFN---------ISQ--  381 (500)
T ss_pred             cccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCC---------ccc--
Confidence            999999999999988999999999999999999999999999999999999988665421111000         000  


Q ss_pred             CCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhcccccc
Q 005812          320 SDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKV  399 (676)
Q Consensus       320 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  399 (676)
                                                      .    ....+.                                     
T Consensus       382 --------------------------------~----~~~~i~-------------------------------------  388 (500)
T KOG0120|consen  382 --------------------------------S----QVPGIP-------------------------------------  388 (500)
T ss_pred             --------------------------------c----ccccch-------------------------------------
Confidence                                            0    000000                                     


Q ss_pred             ccccccCCCCCCCCCCCcccCCCCCCCeEEEcCC--CCCC-C-------HHHHHHHHHhCCceeEEEEeecC---CCCCc
Q 005812          400 SDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNL--PFDL-D-------NEEVKQRFSAFGEVVSFVPVLHQ---VTKRP  466 (676)
Q Consensus       400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL--p~~~-t-------eedl~~~F~~~G~v~~v~i~~~~---~~~~~  466 (676)
                                     .........+...|.+.|+  |.+. .       -|+|+.-|++||.|.+|.|.++.   .....
T Consensus       389 ---------------~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G  453 (500)
T KOG0120|consen  389 ---------------LLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPG  453 (500)
T ss_pred             ---------------hhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCC
Confidence                           0000113334567777776  1111 1       25667788899999999888762   23345


Q ss_pred             ceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEcc
Q 005812          467 KGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKAL  508 (676)
Q Consensus       467 ~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~  508 (676)
                      .|..||+|.+.+++++|+++|+     |..|.||+|...|..
T Consensus       454 ~GkVFVefas~ed~qrA~~~L~-----GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  454 TGKVFVEFADTEDSQRAMEELT-----GRKFANRTVVASYYD  490 (500)
T ss_pred             cccEEEEecChHHHHHHHHHcc-----CceeCCcEEEEEecC
Confidence            7889999999999999999999     999999999999864

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.67  E-value=2.4e-15  Score=139.56  Aligned_cols=202  Identities=25%  Similarity=0.326  Sum_probs=138.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----HHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          424 LQNTIFICNLPFDLDNEEVKQ----RFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~----~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      ++.+|||.||+..+..++|+.    +|++||.|..|...   .+.+.+|.|||.|++.+.|..|+..|+     |+.+.|
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~-----gfpFyg   79 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQ-----GFPFYG   79 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhc-----CCcccC
Confidence            345999999999999999988    99999999998654   356789999999999999999999999     999999


Q ss_pred             cEEEEEEccCchhhhhHhhhhhcccccccCcc-cccccCcc--cCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCC---c
Q 005812          500 RQLTVLKALDKKLAHDKEIDKSKNETNDHRNL-YLAKEGLI--LEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPN---F  573 (676)
Q Consensus       500 r~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~-~~~~~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~---~  573 (676)
                      ++++|.||.++..--.+..-. -.......+. .+...+..  ..+.+..  +.              ...++.|.   .
T Consensus        80 K~mriqyA~s~sdii~~~~~~-~v~~~~k~~~~~~~~~~~~~~~ng~~~~--~~--------------~~~~p~p~~~~~  142 (221)
T KOG4206|consen   80 KPMRIQYAKSDSDIIAQAPGT-FVEKEKKINGEILARIKQPLDTNGHFYN--MN--------------RMNLPPPFLAQM  142 (221)
T ss_pred             chhheecccCccchhhccCce-eccccCccccccccccCCcccccccccc--cc--------------cccCCCCccccC
Confidence            999999999876433221100 0000000000 00000000  0000000  00              00000110   1


Q ss_pred             cccCCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHH
Q 005812          574 HVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRV  653 (676)
Q Consensus       574 ~~~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~  653 (676)
                      ..+...|++.|||..++.+.+..+|.         +|+..+.|+++..           -+|.|||+|.+...|..|+.+
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~---------qf~g~keir~i~~-----------~~~iAfve~~~d~~a~~a~~~  202 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFE---------QFPGFKEIRLIPP-----------RSGIAFVEFLSDRQASAAQQA  202 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHh---------hCcccceeEeccC-----------CCceeEEecchhhhhHHHhhh
Confidence            12346799999999999999999999         6999999998843           479999999999999999999


Q ss_pred             HcCCCCCCCcccCcccccc
Q 005812          654 LNNNPSKLFYHHCFDAADA  672 (676)
Q Consensus       654 lng~~~~~~~~~~~~~~~~  672 (676)
                      |.|...-  +..-..|++|
T Consensus       203 lq~~~it--~~~~m~i~~a  219 (221)
T KOG4206|consen  203 LQGFKIT--KKNTMQITFA  219 (221)
T ss_pred             hccceec--cCceEEeccc
Confidence            9995432  2344444444

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.65  E-value=2e-15  Score=134.00  Aligned_cols=154  Identities=17%  Similarity=0.248  Sum_probs=131.2

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeec
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIK  198 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~  198 (676)
                      +..++|||+|||.++-+.+|.++|.+||.|..|.|..            .....+||||+|+++.+|+.|+..-+|..+.
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~------------r~g~ppfafVeFEd~RDAeDAiygRdGYdyd   71 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKN------------RPGPPPFAFVEFEDPRDAEDAIYGRDGYDYD   71 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEecc------------CCCCCCeeEEEecCccchhhhhhcccccccC
Confidence            4568999999999999999999999999999999642            2344689999999999999999999999999


Q ss_pred             CeEEEEecCCC--------------------------CCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccC
Q 005812          199 GGTVWARQLGG--------------------------EGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNT  252 (676)
Q Consensus       199 ~~~i~v~~~~~--------------------------~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~  252 (676)
                      |..|+|.....                          +....+...|.|++||...+.++|+.++.+-|.|....+.++ 
T Consensus        72 g~rLRVEfprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-  150 (241)
T KOG0105|consen   72 GCRLRVEFPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-  150 (241)
T ss_pred             cceEEEEeccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-
Confidence            99999864321                          233456789999999999999999999999999998888876 


Q ss_pred             CCCCceeEEEEEecCHHHHHHHHHHhCCceeC--CeeEEEE
Q 005812          253 DTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG--KRPIAVD  291 (676)
Q Consensus       253 ~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~--g~~i~v~  291 (676)
                            |++.|+|...++-+-|+.+|..+.+.  |-...+.
T Consensus       151 ------g~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yir  185 (241)
T KOG0105|consen  151 ------GVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIR  185 (241)
T ss_pred             ------cceeeeeeehhhHHHHHHhhccccccCcCcEeeEE
Confidence                  57999999999999999999888763  4444443

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.63  E-value=2.2e-15  Score=136.52  Aligned_cols=83  Identities=34%  Similarity=0.572  Sum_probs=79.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      .+++|||+|||+.+++++|+++|++||.|.++.|+.+..++.++|||||+|.+.++|+.|++.||     +..|+|+.|.
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~ln-----g~~i~Gr~l~  107 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMD-----GKELNGRHIR  107 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcC-----CCEECCEEEE
Confidence            45799999999999999999999999999999999999999999999999999999999999999     9999999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.++..+.
T Consensus       108 V~~a~~~~  115 (144)
T PLN03134        108 VNPANDRP  115 (144)
T ss_pred             EEeCCcCC
Confidence            99987654

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.63  E-value=1.7e-15  Score=148.64  Aligned_cols=288  Identities=18%  Similarity=0.229  Sum_probs=186.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ...+..|..++||+..++.+|..+|...-.....+.......|+..|.|.|.|.+.+.-..|++. +...+.++.|.|..
T Consensus        57 ~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryievYk  135 (508)
T KOG1365|consen   57 ADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEVYK  135 (508)
T ss_pred             cCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceeeec
Confidence            34456777889999999999999998643222222222333577889999999999999999996 88888999999976


Q ss_pred             ecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCC
Q 005812          293 AVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLP  372 (676)
Q Consensus       293 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  372 (676)
                      +....-..-...                                                                 ...
T Consensus       136 a~ge~f~~iagg-----------------------------------------------------------------~s~  150 (508)
T KOG1365|consen  136 ATGEEFLKIAGG-----------------------------------------------------------------TSN  150 (508)
T ss_pred             cCchhheEecCC-----------------------------------------------------------------ccc
Confidence            654321110000                                                                 000


Q ss_pred             CCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhC---
Q 005812          373 SLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAF---  449 (676)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~---  449 (676)
                                                          ..      .........-.|.+++||+++++.||.++|...   
T Consensus       151 ------------------------------------e~------~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv  188 (508)
T KOG1365|consen  151 ------------------------------------EA------APFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPV  188 (508)
T ss_pred             ------------------------------------cC------CCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcc
Confidence                                                00      000000112478899999999999999999632   


Q ss_pred             -CceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhhhHhhhhhccccccc
Q 005812          450 -GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDH  528 (676)
Q Consensus       450 -G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~~~~~~~~~~~~~~~  528 (676)
                       |.++.|.++.. .+|+.+|-|||.|..+++|+.||.+.      .-.|+-|.|.+..+-..+-.+......        
T Consensus       189 ~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~kh------rq~iGqRYIElFRSTaaEvqqvlnr~~--------  253 (508)
T KOG1365|consen  189 TGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRKH------RQNIGQRYIELFRSTAAEVQQVLNREV--------  253 (508)
T ss_pred             cCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHHH------HHHHhHHHHHHHHHhHHHHHHHHHhhc--------
Confidence             34556644444 46899999999999999999999874      366777788775532221111111000        


Q ss_pred             CcccccccCcccC-CCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCeEEEecCCcccCHHHHHHHHHHHHHhhhc
Q 005812          529 RNLYLAKEGLILE-GTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRAS  607 (676)
Q Consensus       529 ~~~~~~~~g~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~  607 (676)
                            .++.+.. ++|...++ +.              .+-.+  ..++.+|.+|+||+.+|.++|..||.++...+--
T Consensus       254 ------s~pLi~~~~sp~~p~~-p~--------------~~~p~--~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f  310 (508)
T KOG1365|consen  254 ------SEPLIPGLTSPLLPGG-PA--------------RLVPP--TRSKDCVRLRGLPYEATVEDILDFLGDFATDIRF  310 (508)
T ss_pred             ------cccccCCCCCCCCCCC-cc--------------ccCCC--CCCCCeeEecCCChhhhHHHHHHHHHHHhhhccc
Confidence                  0011110 11110000 00              00001  1135789999999999999999999987544311


Q ss_pred             ccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCC
Q 005812          608 KQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPS  659 (676)
Q Consensus       608 ~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~  659 (676)
                            .-|++..+       .+|+..|.|||+|.+.+.|..|+...+++.+
T Consensus       311 ------~gVHmv~N-------~qGrPSGeAFIqm~nae~a~aaaqk~hk~~m  349 (508)
T KOG1365|consen  311 ------QGVHMVLN-------GQGRPSGEAFIQMRNAERARAAAQKCHKKLM  349 (508)
T ss_pred             ------ceeEEEEc-------CCCCcChhhhhhhhhhHHHHHHHHHHHHhhc
Confidence                  12555554       4689999999999999999999999887643

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.61  E-value=5.2e-15  Score=134.10  Aligned_cols=85  Identities=27%  Similarity=0.439  Sum_probs=80.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|+.++.+++++|||||+|.+.++|+.|++.|++..|.|+.|+|.|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            44567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 005812          293 AVPKN  297 (676)
Q Consensus       293 a~~~~  297 (676)
                      +.++.
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            97654

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.61  E-value=2e-14  Score=127.61  Aligned_cols=170  Identities=22%  Similarity=0.286  Sum_probs=127.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||.++-+.||.++|-+||.|..|.+-..   -...+||||+|+++.+|..|+..-+     |.-++|+.|.|
T Consensus         6 ~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRd-----GYdydg~rLRV   77 (241)
T KOG0105|consen    6 SRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRD-----GYDYDGCRLRV   77 (241)
T ss_pred             cceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhccc-----ccccCcceEEE
Confidence            589999999999999999999999999999876433   2357899999999999999999999     99999999999


Q ss_pred             EEccCchhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCeEEEec
Q 005812          505 LKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYN  584 (676)
Q Consensus       505 ~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~V~n  584 (676)
                      .++..-....            +.+..|.-...   .+...   .                 .-..|....+..+|.|.+
T Consensus        78 Efprggr~s~------------~~~G~y~gggr---gGgg~---g-----------------g~rgppsrrSe~RVvVsG  122 (241)
T KOG0105|consen   78 EFPRGGRSSS------------DRRGSYSGGGR---GGGGG---G-----------------GRRGPPSRRSEYRVVVSG  122 (241)
T ss_pred             EeccCCCccc------------ccccccCCCCC---CCCCC---C-----------------cccCCcccccceeEEEec
Confidence            9976532111            11111100000   00000   0                 001122222446899999


Q ss_pred             CCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCC
Q 005812          585 LPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPS  659 (676)
Q Consensus       585 lp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~  659 (676)
                      ||.+.+.++|++...+         -|.|-...+.+|             |++.|+|...|+-.-|++.|.....
T Consensus       123 Lp~SgSWQDLKDHmRe---------aGdvCfadv~rD-------------g~GvV~~~r~eDMkYAvr~ld~~~~  175 (241)
T KOG0105|consen  123 LPPSGSWQDLKDHMRE---------AGDVCFADVQRD-------------GVGVVEYLRKEDMKYAVRKLDDQKF  175 (241)
T ss_pred             CCCCCchHHHHHHHHh---------hCCeeeeeeecc-------------cceeeeeeehhhHHHHHHhhccccc
Confidence            9999999999999996         577766666655             7999999999999999999987644

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.60  E-value=2.1e-14  Score=141.07  Aligned_cols=280  Identities=22%  Similarity=0.313  Sum_probs=190.0

Q ss_pred             cEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeE
Q 005812          122 RTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGT  201 (676)
Q Consensus       122 ~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~  201 (676)
                      .-|...+|||..+..+|-.+|...-...--+.. .        ++-.|+..|.|.|+|.+.|.-..|++. +..-+.++.
T Consensus        61 vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aK-O--------G~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ry  130 (508)
T KOG1365|consen   61 VVVRARGLPWQSSDQDIARFFKGLNIANGGRAL-C--------LNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRY  130 (508)
T ss_pred             eEEEecCCCCCcccCCHHHHHhhhhccccceee-e--------ehhhhccccceEEEecCchhhhhhhHh-hhhhccCCc
Confidence            346678999999999999999854211111100 0        123477788999999999999999884 555666676


Q ss_pred             EEEecCCCC----------------CCCCCCcEEEEcCCCCCCCHHHHHHhhcc---C-CceEEEEEcccCCCCCceeEE
Q 005812          202 VWARQLGGE----------------GSKTQKWKLIIRNIPFKAKVNEIKDMFSP---V-GLVWNVYIPHNTDTGLSKGFA  261 (676)
Q Consensus       202 i~v~~~~~~----------------~~~~~~~~v~V~nLp~~~~e~~l~~~F~~---~-G~i~~v~i~~~~~~~~~~g~a  261 (676)
                      |.+-...+.                .++...-.|.+++||+++++.|+.++|.+   . |..+.|.++..+ +|+..|-|
T Consensus       131 ievYka~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdA  209 (508)
T KOG1365|consen  131 IEVYKATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDA  209 (508)
T ss_pred             eeeeccCchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccce
Confidence            665332211                11223456778899999999999999963   2 345566666653 78899999


Q ss_pred             EEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccc
Q 005812          262 FVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEK  341 (676)
Q Consensus       262 fV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (676)
                      ||.|..+++|+.||.+ |...++-|-|.+-.+.                                               
T Consensus       210 Fvlfa~ee~aq~aL~k-hrq~iGqRYIElFRST-----------------------------------------------  241 (508)
T KOG1365|consen  210 FVLFACEEDAQFALRK-HRQNIGQRYIELFRST-----------------------------------------------  241 (508)
T ss_pred             EEEecCHHHHHHHHHH-HHHHHhHHHHHHHHHh-----------------------------------------------
Confidence            9999999999999997 7777777767664432                                               


Q ss_pred             cCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCC
Q 005812          342 EDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGE  421 (676)
Q Consensus       342 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  421 (676)
                                  ....++.+++.... +-++..... ..+.+                               ++.-...
T Consensus       242 ------------aaEvqqvlnr~~s~-pLi~~~~sp-~~p~~-------------------------------p~~~~p~  276 (508)
T KOG1365|consen  242 ------------AAEVQQVLNREVSE-PLIPGLTSP-LLPGG-------------------------------PARLVPP  276 (508)
T ss_pred             ------------HHHHHHHHHhhccc-cccCCCCCC-CCCCC-------------------------------ccccCCC
Confidence                        22334444433211 000000000 00000                               0000011


Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCc-eeE--EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGE-VVS--FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK  498 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~-v~~--v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~  498 (676)
                      .....+|.+++||+..+.|||.++|..|-. |..  |.++.+ .-|++.|-|||+|.+.++|..|....+     ...+.
T Consensus       277 ~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~h-----k~~mk  350 (508)
T KOG1365|consen  277 TRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCH-----KKLMK  350 (508)
T ss_pred             CCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHH-----Hhhcc
Confidence            222469999999999999999999999863 444  555555 458999999999999999999999998     77778


Q ss_pred             CcEEEEEEccCch
Q 005812          499 GRQLTVLKALDKK  511 (676)
Q Consensus       499 gr~l~v~~a~~k~  511 (676)
                      +|.|.|..+.-.+
T Consensus       351 ~RYiEvfp~S~ee  363 (508)
T KOG1365|consen  351 SRYIEVFPCSVEE  363 (508)
T ss_pred             cceEEEeeccHHH
Confidence            9999998876543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.58  E-value=7.8e-14  Score=127.70  Aligned_cols=84  Identities=20%  Similarity=0.283  Sum_probs=70.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEccc-CCCCCceeEEEEEecCHHHHHHHHHHhCCcee---CCeeEEE
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHN-TDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF---GKRPIAV  290 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~-~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~---~g~~i~v  290 (676)
                      .-++|||.+||.++...+|..+|..|-..+.+.+... +.....+-+|||.|.+..+|..|++.|||..|   .+..|++
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            3589999999999999999999999877777766442 22233557999999999999999999999999   5889999


Q ss_pred             EEecCCCC
Q 005812          291 DWAVPKNI  298 (676)
Q Consensus       291 ~~a~~~~~  298 (676)
                      ++++....
T Consensus       113 ElAKSNtK  120 (284)
T KOG1457|consen  113 ELAKSNTK  120 (284)
T ss_pred             eehhcCcc
Confidence            99876543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.57  E-value=9.6e-14  Score=127.10  Aligned_cols=212  Identities=23%  Similarity=0.247  Sum_probs=131.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEee-cCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec---Cc
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVL-HQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK---GR  500 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~-~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~---gr  500 (676)
                      -++|||.+||.++-..+|..+|..|-..+.+.+-. ++.....+-+|||+|.+..+|..|+.+||     |..|+   +.
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLN-----GvrFDpE~~s  108 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALN-----GVRFDPETGS  108 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhc-----CeeeccccCc
Confidence            58999999999999999999999997777765433 33344556899999999999999999999     99997   78


Q ss_pred             EEEEEEccCchhhhhHhhhhhcc----cccccCcccc-------cccCcc----cCCCCCCCCCChhH-------HHHHH
Q 005812          501 QLTVLKALDKKLAHDKEIDKSKN----ETNDHRNLYL-------AKEGLI----LEGTPAAEGVSDDD-------MSKRQ  558 (676)
Q Consensus       501 ~l~v~~a~~k~~~~~~~~~~~~~----~~~~~~~~~~-------~~~g~~----~~~~~~~~~~~~~~-------~~~~~  558 (676)
                      .|+|++|+++....+...-....    -..+.++...       ..++..    ....-.+..+.+.+       .+...
T Consensus       109 tLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~  188 (284)
T KOG1457|consen  109 TLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDS  188 (284)
T ss_pred             eeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhh
Confidence            99999998865433221111000    0000000000       000000    00000001111111       11110


Q ss_pred             HHHH--HHhhcCCC-CCccccCCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcce
Q 005812          559 MLHE--KKMTKLQS-PNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRG  635 (676)
Q Consensus       559 ~~~~--~~~~~~~~-p~~~~~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g  635 (676)
                      +...  ...++.+. -.......+|||-||...+||++|+.+|+.         |.....++|.-.          ....
T Consensus       189 ~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~---------~~gf~~l~~~~~----------~g~~  249 (284)
T KOG1457|consen  189 KAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSR---------YPGFHILKIRAR----------GGMP  249 (284)
T ss_pred             cCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHh---------CCCceEEEEecC----------CCcc
Confidence            0000  00011100 011123357999999999999999999995         777666666421          2356


Q ss_pred             EEEEEeCChHHHHHHHHHHcCCCCC
Q 005812          636 VAFVEFTEHQHALVALRVLNNNPSK  660 (676)
Q Consensus       636 ~afV~F~~~~~A~~Ai~~lng~~~~  660 (676)
                      .|||+|.+.+.|..||..|+|+-+.
T Consensus       250 vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  250 VAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             eEeecHHHHHHHHHHHHHhhcceec
Confidence            8999999999999999999998654

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.53  E-value=3.2e-13  Score=131.83  Aligned_cols=199  Identities=20%  Similarity=0.331  Sum_probs=140.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceE--------EEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVW--------NVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK  285 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~--------~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g  285 (676)
                      ..+..|||.|||.++|.+++.++|+++|.|.        .|++-++. .|+.+|=|++.|-..++...|++.|++..|.|
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            3467799999999999999999999999875        36777764 59999999999999999999999999999999


Q ss_pred             eeEEEEEecCCCC--CCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhc
Q 005812          286 RPIAVDWAVPKNI--YSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNK  363 (676)
Q Consensus       286 ~~i~v~~a~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  363 (676)
                      +.|+|+.|+-...  +........                                      ............++.+..
T Consensus       211 ~~~rVerAkfq~Kge~~~~~k~k~--------------------------------------k~~~~kk~~k~q~k~~dw  252 (382)
T KOG1548|consen  211 KKLRVERAKFQMKGEYDASKKEKG--------------------------------------KCKDKKKLKKQQQKLLDW  252 (382)
T ss_pred             cEEEEehhhhhhccCcCccccccc--------------------------------------ccccHHHHHHHHHhhccc
Confidence            9999998753321  111111000                                      000000001111111111


Q ss_pred             ccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCC----CCCC-
Q 005812          364 LTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLP----FDLD-  438 (676)
Q Consensus       364 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp----~~~t-  438 (676)
                      ...                                          .       .........++|.|+||=    +..+ 
T Consensus       253 ~pd------------------------------------------~-------~~~sk~r~~~tVi~kn~Ftp~~~~~~~  283 (382)
T KOG1548|consen  253 RPD------------------------------------------R-------DDPSKARADRTVILKNMFTPEDFEKNP  283 (382)
T ss_pred             CCC------------------------------------------c-------cccccccCCcEEEeeecCCHHHhccCH
Confidence            000                                          0       000112234799999991    2223 


Q ss_pred             ------HHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccC
Q 005812          439 ------NEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALD  509 (676)
Q Consensus       439 ------eedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~  509 (676)
                            .++|++-+++||.|.+|.|. +   ..+.|.+-|.|.+.++|..|++.|+     |..|+||.|+.+..--
T Consensus       284 ~l~~dlkedl~eec~K~G~v~~vvv~-d---~hPdGvvtV~f~n~eeA~~ciq~m~-----GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  284 DLLNDLKEDLTEECEKFGQVRKVVVY-D---RHPDGVVTVSFRNNEEADQCIQTMD-----GRWFDGRQLTASIWDG  351 (382)
T ss_pred             HHHHHHHHHHHHHHHHhCCcceEEEe-c---cCCCceeEEEeCChHHHHHHHHHhc-----CeeecceEEEEEEeCC
Confidence                  56777889999999999554 3   3568999999999999999999999     9999999999987543

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=99.52  E-value=7.2e-13  Score=139.48  Aligned_cols=161  Identities=14%  Similarity=0.045  Sum_probs=116.6

Q ss_pred             EEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCc-cceEEEEeCCHHHHHHHHHHhCCCeecCeE
Q 005812          123 TVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCK-MDASAVLYTTVKSACASVALLHQKEIKGGT  201 (676)
Q Consensus       123 ~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~-~g~afV~F~~~~~A~~A~~~l~~~~~~~~~  201 (676)
                      .+-+.+.+...+..+++++|... .|..+.|..+          +-+.+ .|-+||.|....++++|+. -|...+-.+.
T Consensus       313 y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~----------~v~~~~tG~~~v~f~~~~~~q~A~~-rn~~~~~~R~  380 (944)
T KOG4307|consen  313 YNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSEN----------RVAPPQTGRKTVMFTPQAPFQNAFT-RNPSDDVNRP  380 (944)
T ss_pred             eeeecccccccccchhhhhcCcc-cccccchhhh----------hcCCCcCCceEEEecCcchHHHHHh-cCchhhhhcc
Confidence            45567888889999999998743 3333333222          22333 7889999999999999987 3555555565


Q ss_pred             EEEecCC------------------------------------CC---CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCc
Q 005812          202 VWARQLG------------------------------------GE---GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGL  242 (676)
Q Consensus       202 i~v~~~~------------------------------------~~---~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~  242 (676)
                      +.+.+..                                    +.   ........|||..||..+++.++..+|...-.
T Consensus       381 ~q~~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~  460 (944)
T KOG4307|consen  381 FQTGPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAA  460 (944)
T ss_pred             eeecCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhh
Confidence            5442110                                    00   01123579999999999999999999998777


Q ss_pred             eEE-EEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          243 VWN-VYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       243 i~~-v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      |++ |.|.+.+ +++.++.|||.|..++++..|+..-+...++.+.|+|.-...+
T Consensus       461 Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~  514 (944)
T KOG4307|consen  461 VEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADY  514 (944)
T ss_pred             hhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeechhhH
Confidence            777 5555544 6778899999999999999998876777788899999865433

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

Probab=99.51  E-value=4.7e-14  Score=131.34  Aligned_cols=85  Identities=31%  Similarity=0.663  Sum_probs=81.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      ...+.++|-|.|||.+++|++|+++|.+||.|.+|.|.+++.+|.++|||||.|.+.++|.+||..|||.-+..-.|+|+
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            34467899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCC
Q 005812          292 WAVPK  296 (676)
Q Consensus       292 ~a~~~  296 (676)
                      |++|+
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99886

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.50  E-value=7.6e-13  Score=129.24  Aligned_cols=193  Identities=14%  Similarity=0.225  Sum_probs=134.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCC
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS--------FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLG  494 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~--------v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g  494 (676)
                      ..+..|||.|||.++|.+++.++|+++|.|..        |++.++. .|..+|-|+++|.-.++..-|++.|+     +
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilD-----e  205 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILD-----E  205 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhC-----c
Confidence            34567999999999999999999999998865        6777775 48999999999999999999999999     9


Q ss_pred             eeecCcEEEEEEccCchhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHH----HhhcCCC
Q 005812          495 IFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEK----KMTKLQS  570 (676)
Q Consensus       495 ~~l~gr~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~  570 (676)
                      ..|.|+.|+|..|+=-..       ......                .-+   .....+..+....++.    .+.. ..
T Consensus       206 ~~~rg~~~rVerAkfq~K-------ge~~~~----------------~k~---k~k~~~~kk~~k~q~k~~dw~pd~-~~  258 (382)
T KOG1548|consen  206 DELRGKKLRVERAKFQMK-------GEYDAS----------------KKE---KGKCKDKKKLKKQQQKLLDWRPDR-DD  258 (382)
T ss_pred             ccccCcEEEEehhhhhhc-------cCcCcc----------------ccc---ccccccHHHHHHHHHhhcccCCCc-cc
Confidence            999999999998763110       000000                000   0000111111111111    0111 11


Q ss_pred             CCccccCCeEEEecC--CcccC-HHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHH
Q 005812          571 PNFHVSRTRLVIYNL--PKSMT-EKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHA  647 (676)
Q Consensus       571 p~~~~~~~~l~V~nl--p~~~t-e~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A  647 (676)
                      |......++|.++|+  |.... ..+|..-+.+.++.+|. .||.|.+|.+.-.          .+.|.+.|.|.+.++|
T Consensus       259 ~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~-K~G~v~~vvv~d~----------hPdGvvtV~f~n~eeA  327 (382)
T KOG1548|consen  259 PSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECE-KFGQVRKVVVYDR----------HPDGVVTVSFRNNEEA  327 (382)
T ss_pred             cccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHH-HhCCcceEEEecc----------CCCceeEEEeCChHHH
Confidence            333334578999999  55443 33555566666777787 5999999977532          4579999999999999


Q ss_pred             HHHHHHHcCCCC
Q 005812          648 LVALRVLNNNPS  659 (676)
Q Consensus       648 ~~Ai~~lng~~~  659 (676)
                      ..+|+.|+|+..
T Consensus       328 ~~ciq~m~GR~f  339 (382)
T KOG1548|consen  328 DQCIQTMDGRWF  339 (382)
T ss_pred             HHHHHHhcCeee
Confidence            999999999843

>PF00076 RRM_1: RNA recognition motif

Probab=99.49  E-value=2e-13  Score=108.30  Aligned_cols=70  Identities=30%  Similarity=0.572  Sum_probs=66.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       428 l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      |||+|||..+++++|+++|+.||.|..+.++.+ .++.++++|||+|.+.++|.+|++.|+     |..++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~-----g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELN-----GKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHT-----TEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcC-----CCEECccCcC
Confidence            799999999999999999999999999999887 678899999999999999999999999     9999999985

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.48  E-value=6.5e-14  Score=131.72  Aligned_cols=166  Identities=23%  Similarity=0.409  Sum_probs=130.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      ..+||++||+.+.+.+|..+|..||.|..+.+..        ||+||+|.+.-+|..|+..|++..|+|-.+.|+|+...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            3699999999999999999999999999987743        78999999999999999999999999988999998654


Q ss_pred             CCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCC
Q 005812          297 NIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSD  376 (676)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  376 (676)
                      ........                                                                        
T Consensus        74 ~~~~g~~~------------------------------------------------------------------------   81 (216)
T KOG0106|consen   74 RRGRGRPR------------------------------------------------------------------------   81 (216)
T ss_pred             ccccCCCC------------------------------------------------------------------------
Confidence            31110000                                                                        


Q ss_pred             ccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEE
Q 005812          377 DSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFV  456 (676)
Q Consensus       377 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~  456 (676)
                            +                      ..+..   -...........+.++|.|++..+.+++|.++|+.+|.+.+..
T Consensus        82 ------~----------------------g~r~~---~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~  130 (216)
T KOG0106|consen   82 ------G----------------------GDRRS---DSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVD  130 (216)
T ss_pred             ------C----------------------CCccc---hhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhh
Confidence                  0                      00000   0000000122357899999999999999999999999996553


Q ss_pred             EeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEE
Q 005812          457 PVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLK  506 (676)
Q Consensus       457 i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~  506 (676)
                      +        ..+++||+|.+.++|.+|+..|+     +..+.|+.|.+..
T Consensus       131 ~--------~~~~~~v~Fs~~~da~ra~~~l~-----~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  131 A--------RRNFAFVEFSEQEDAKRALEKLD-----GKKLNGRRISVEK  167 (216)
T ss_pred             h--------hccccceeehhhhhhhhcchhcc-----chhhcCceeeecc
Confidence            2        46789999999999999999999     9999999999944

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

Probab=99.48  E-value=2.1e-13  Score=127.00  Aligned_cols=82  Identities=21%  Similarity=0.291  Sum_probs=79.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      ..++|.|.||+.++++.+|+++|.+||.|..|+|.+|+.+|.++|||||.|.+.++|.+|+..||     |+-++.-.|.
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~Ln-----G~gyd~LILr  262 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLN-----GYGYDNLILR  262 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHcc-----CcccceEEEE
Confidence            56899999999999999999999999999999999999999999999999999999999999999     9999999999


Q ss_pred             EEEccCc
Q 005812          504 VLKALDK  510 (676)
Q Consensus       504 v~~a~~k  510 (676)
                      |.|+.|+
T Consensus       263 vEwskP~  269 (270)
T KOG0122|consen  263 VEWSKPS  269 (270)
T ss_pred             EEecCCC
Confidence            9999875

>PF00076 RRM_1: RNA recognition motif

Probab=99.47  E-value=2.6e-13  Score=107.63  Aligned_cols=70  Identities=37%  Similarity=0.668  Sum_probs=67.0

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEE
Q 005812          219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIA  289 (676)
Q Consensus       219 v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~  289 (676)
                      |||+|||.++++++|+++|+.||.|..+.+..+ .++..+|||||+|.+.++|..|++.|+|..+.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999987 5788999999999999999999999999999999985

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.46  E-value=1.9e-13  Score=114.24  Aligned_cols=79  Identities=25%  Similarity=0.550  Sum_probs=76.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      .+++|||+||+..++|++|.++|++.|.|..|.+-.|+.+..+.|||||+|.+.++|..|++-++|+.++.++|+++|.
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            5679999999999999999999999999999999999989999999999999999999999999999999999999985

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.45  E-value=5.7e-13  Score=107.12  Aligned_cols=90  Identities=22%  Similarity=0.344  Sum_probs=79.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ...++.|||+|||+++|.|+..++|.+||.|+.++|-..+   ..+|.|||.|++..+|.+|+.+|+     |..+.++.
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhls-----g~n~~~ry   86 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLS-----GYNVDNRY   86 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhc-----ccccCCce
Confidence            3456899999999999999999999999999999885443   468999999999999999999999     99999999


Q ss_pred             EEEEEccCchhhhhHhhh
Q 005812          502 LTVLKALDKKLAHDKEID  519 (676)
Q Consensus       502 l~v~~a~~k~~~~~~~~~  519 (676)
                      |.|-+..+.+........
T Consensus        87 l~vlyyq~~~~~~~~~~~  104 (124)
T KOG0114|consen   87 LVVLYYQPEDAFKLMDSR  104 (124)
T ss_pred             EEEEecCHHHHHHHHHhH
Confidence            999999887765554433

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=99.41  E-value=2.3e-11  Score=128.30  Aligned_cols=163  Identities=10%  Similarity=-0.007  Sum_probs=106.1

Q ss_pred             cCCCCcccceEEEEecCHHHHHHHHHHhCCceecCeEEEEeeccccchHHHhhhhhchhhhhhhhhhccCC-CCCccccc
Q 005812            4 KKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAEDIEKTMDN-KDGVISGA   82 (676)
Q Consensus         4 ~~~tg~s~G~afV~F~~~edA~~Al~~~~g~~i~gr~i~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~   82 (676)
                      +..-+...|.+||.|....++++|++. |.+.+..|.+.|.+.....    +........+..+  ..+.+ +..-++. 
T Consensus       345 ~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~g~~~----~~~a~~~~~~~~~--~~~~~~hg~p~~~-  416 (944)
T KOG4307|consen  345 NRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPPGNLG----RNGAPPFQAGVPP--PVIQNNHGRPIAP-  416 (944)
T ss_pred             hhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCCCccc----cccCccccccCCC--CcccccCCCCCCC-
Confidence            334455589999999999999999999 8899999999998875441    2111111111111  11111 1111110 


Q ss_pred             ccccchhhccCCCCCCCcccccCcccCCCCccchhcccCcEEEEcCCCccccHHHHHHHhhcCCCeEE-EEeeCCchhhh
Q 005812           83 EKHSSKLLESGKTVKPRKAATLGIDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCS-VTYPLPKEELE  161 (676)
Q Consensus        83 ~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~-v~~~~~~~~~~  161 (676)
                                     +|-....+..+.-      ....+.+|||..||..+++.++.++|...-.|++ |.|..      
T Consensus       417 ---------------pr~~~~~gq~vp~------P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~------  469 (944)
T KOG4307|consen  417 ---------------PRAMVRPGQNVPF------PGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTR------  469 (944)
T ss_pred             ---------------cccccCCCCCCCC------CCCccceEEeccCCccccccchhhhhhhhhhhhheeEecc------
Confidence                           1111111111111      2245779999999999999999999999888888 44432      


Q ss_pred             hcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeEEEEe
Q 005812          162 QHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWAR  205 (676)
Q Consensus       162 ~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~i~v~  205 (676)
                          ...++-++.|||.|..++++.+|...-+...++-+.|+|+
T Consensus       470 ----~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  470 ----LPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVD  509 (944)
T ss_pred             ----CCcccccchhhheeccccccchhhhcccccccCceEEEee
Confidence                2457788999999999999999987656666666666654

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.41  E-value=1.4e-12  Score=103.49  Aligned_cols=70  Identities=29%  Similarity=0.500  Sum_probs=64.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       428 l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      |||+|||+.+++++|+++|+.||.|..+.+..++. +.++|+|||+|.++++|.+|+..++     +..|+|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~-----~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLN-----GKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHT-----TEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCC-----CcEECCEEcC
Confidence            79999999999999999999999999999998876 8899999999999999999999999     9999999884

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.39  E-value=2.6e-12  Score=101.92  Aligned_cols=70  Identities=34%  Similarity=0.632  Sum_probs=64.7

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEE
Q 005812          219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIA  289 (676)
Q Consensus       219 v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~  289 (676)
                      |||+|||+++++++|+++|+.||.|..+.+..++. +..+|+|||+|.+.++|.+|++.+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999876 88999999999999999999999999999999874

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.39  E-value=8e-13  Score=110.55  Aligned_cols=79  Identities=23%  Similarity=0.366  Sum_probs=74.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      +++|||+||.+-++||.|.++|+++|.|+.|..-.|+.+..+.|||||+|-+.++|..|++-++     ++.|+.++|.+
T Consensus        36 S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryis-----gtrLddr~ir~  110 (153)
T KOG0121|consen   36 SCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYIS-----GTRLDDRPIRI  110 (153)
T ss_pred             cceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhc-----cCcccccceee
Confidence            6899999999999999999999999999998666788888899999999999999999999999     99999999999


Q ss_pred             EEcc
Q 005812          505 LKAL  508 (676)
Q Consensus       505 ~~a~  508 (676)
                      .|..
T Consensus       111 D~D~  114 (153)
T KOG0121|consen  111 DWDA  114 (153)
T ss_pred             eccc
Confidence            9954

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.37  E-value=1.2e-12  Score=126.84  Aligned_cols=102  Identities=28%  Similarity=0.409  Sum_probs=87.8

Q ss_pred             CCCeecCeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHH
Q 005812          193 HQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAE  272 (676)
Q Consensus       193 ~~~~~~~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~  272 (676)
                      ++....|-.+..............++|+|.|||+...+-||+.+|.+||.|.+|.|+.+.  .-+||||||+|++.+||+
T Consensus        73 ~~~~t~g~~~~~~~st~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dad  150 (376)
T KOG0125|consen   73 NGAPTDGQPIQTQPSTNSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADAD  150 (376)
T ss_pred             CCCCCCCCccccCCCCcCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHH
Confidence            444455556666555555566677899999999999999999999999999999999874  338999999999999999


Q ss_pred             HHHHHhCCceeCCeeEEEEEecCC
Q 005812          273 SAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       273 ~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      +|.++|||+.+.||+|.|..+.++
T Consensus       151 RARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  151 RARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             HHHHHhhcceeeceEEEEeccchh
Confidence            999999999999999999998776

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.37  E-value=9.5e-13  Score=122.46  Aligned_cols=78  Identities=32%  Similarity=0.520  Sum_probs=73.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      +.|||+||++.+..++|+++|++||.|.++.|+.|+.+|+++|||||+|.+.++|.+|++..|      -.|+||+-.|.
T Consensus        13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~------piIdGR~aNcn   86 (247)
T KOG0149|consen   13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN------PIIDGRKANCN   86 (247)
T ss_pred             EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC------Ccccccccccc
Confidence            689999999999999999999999999999999999999999999999999999999998876      79999999988


Q ss_pred             EccC
Q 005812          506 KALD  509 (676)
Q Consensus       506 ~a~~  509 (676)
                      +|.-
T Consensus        87 lA~l   90 (247)
T KOG0149|consen   87 LASL   90 (247)
T ss_pred             hhhh
Confidence            8654

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.36  E-value=1.3e-12  Score=123.13  Aligned_cols=145  Identities=28%  Similarity=0.426  Sum_probs=124.0

Q ss_pred             EEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeEE
Q 005812          123 TVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTV  202 (676)
Q Consensus       123 ~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~i  202 (676)
                      .+||++||+.+.+.+|..+|..||.+..+.+.                 .||+||+|.+..+|..|+..||+..|.|..+
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk-----------------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~   65 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK-----------------NGFGFVEFEDPRDADDAVHDLDGKELCGERL   65 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee-----------------cccceeccCchhhhhcccchhcCceecceee
Confidence            58999999999999999999999999988743                 5789999999999999999999999999885


Q ss_pred             EEecCCC------C--------------CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEE
Q 005812          203 WARQLGG------E--------------GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAF  262 (676)
Q Consensus       203 ~v~~~~~------~--------------~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~af  262 (676)
                      .+.....      .              ......+.++|.+++..+.+.+|..+|..+|.+....+        ..+++|
T Consensus        66 vve~~r~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~  137 (216)
T KOG0106|consen   66 VVEHARGKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAF  137 (216)
T ss_pred             eeecccccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccc
Confidence            5432210      0              01234689999999999999999999999999965444        346799


Q ss_pred             EEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          263 VKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       263 V~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      |+|++.++|..|+..|++..+.++.|.+..
T Consensus       138 v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  138 VEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             eeehhhhhhhhcchhccchhhcCceeeecc
Confidence            999999999999999999999999999943

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=99.35  E-value=2.7e-12  Score=133.42  Aligned_cols=161  Identities=17%  Similarity=0.144  Sum_probs=113.5

Q ss_pred             cchhcccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhC
Q 005812          114 CSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLH  193 (676)
Q Consensus       114 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~  193 (676)
                      ++.+....++|+|-|||.++++++|+.+|+.||+|..|+              ..-..+|..||+|.+..+|+.|++.|+
T Consensus        68 p~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir--------------~t~~~~~~~~v~FyDvR~A~~Alk~l~  133 (549)
T KOG4660|consen   68 PSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIR--------------ETPNKRGIVFVEFYDVRDAERALKALN  133 (549)
T ss_pred             CCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhh--------------cccccCceEEEEEeehHhHHHHHHHHH
Confidence            344456778999999999999999999999999999987              234557889999999999999999999


Q ss_pred             CCeecCeEEEEecCCC-----------------------CCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcc
Q 005812          194 QKEIKGGTVWARQLGG-----------------------EGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPH  250 (676)
Q Consensus       194 ~~~~~~~~i~v~~~~~-----------------------~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~  250 (676)
                      +..+.|+.+. ++...                       .........+ ++.|++.....-++..|..+|.+.. +.. 
T Consensus       134 ~~~~~~~~~k-~~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~-~g~l~P~~s~~~~~~~~~~~~~~~~-~~~-  209 (549)
T KOG4660|consen  134 RREIAGKRIK-RPGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQL-FGMLSPTRSSILLEHISSVDGSSPG-RET-  209 (549)
T ss_pred             HHHhhhhhhc-CCCcccccchhcccchhhhhccchhhcCCCCCCcCCcc-eeeeccchhhhhhhcchhccCcccc-ccc-
Confidence            9999998876 21110                       0011112222 2338888887666777777887765 222 


Q ss_pred             cCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCC
Q 005812          251 NTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKN  297 (676)
Q Consensus       251 ~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~  297 (676)
                          +.-.-.-|+.|.+..++..+.... |..+.+....+.++.+..
T Consensus       210 ----~~~~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~~g  251 (549)
T KOG4660|consen  210 ----PLLNHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSGPGG  251 (549)
T ss_pred             ----cchhhhhhhhhccccchhhcccCC-ceecCCCCceEEecCCCc
Confidence                212224577888888876666543 666666666677766643

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.35  E-value=4.6e-12  Score=122.58  Aligned_cols=76  Identities=18%  Similarity=0.263  Sum_probs=70.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|+.||.|.+|.|+.+..   ++|||||+|.++++|..|+. |+     |..|.|+.|.|
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-Ln-----G~~l~gr~V~V   74 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LS-----GATIVDQSVTI   74 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hc-----CCeeCCceEEE
Confidence            47999999999999999999999999999999988753   57999999999999999994 99     99999999999


Q ss_pred             EEccC
Q 005812          505 LKALD  509 (676)
Q Consensus       505 ~~a~~  509 (676)
                      .++..
T Consensus        75 t~a~~   79 (260)
T PLN03120         75 TPAED   79 (260)
T ss_pred             EeccC
Confidence            99764

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.34  E-value=1e-11  Score=127.36  Aligned_cols=80  Identities=34%  Similarity=0.663  Sum_probs=77.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      .++|||+|||..+++++|+++|..||.|..+.+..++.++.++|||||+|.+.++|..|+..+++..|.|+.|.|.++.+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            59999999999999999999999999999999999988999999999999999999999999999999999999999754

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.34  E-value=4e-12  Score=123.30  Aligned_cols=79  Identities=23%  Similarity=0.525  Sum_probs=74.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|+|.||||..-+.||+.+|.+||.|.+|.|+.+.  .-+||||||+|+++++|++|.++||     |.++.||+|.|
T Consensus        96 pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LH-----gt~VEGRkIEV  168 (376)
T KOG0125|consen   96 PKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELH-----GTVVEGRKIEV  168 (376)
T ss_pred             CceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhh-----cceeeceEEEE
Confidence            4799999999999999999999999999999999874  3479999999999999999999999     99999999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      ..|-.+
T Consensus       169 n~ATar  174 (376)
T KOG0125|consen  169 NNATAR  174 (376)
T ss_pred             eccchh
Confidence            998765

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.34  E-value=2.1e-12  Score=114.47  Aligned_cols=78  Identities=29%  Similarity=0.496  Sum_probs=72.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ...+.|||+||+..+++.+|...|..||.|..|+|..+     ..|||||+|+++.+|..|+..|+|..|+|..|.|+++
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            44789999999999999999999999999999999886     5799999999999999999999999999999999998


Q ss_pred             cCC
Q 005812          294 VPK  296 (676)
Q Consensus       294 ~~~  296 (676)
                      .-.
T Consensus        83 ~G~   85 (195)
T KOG0107|consen   83 TGR   85 (195)
T ss_pred             cCC
Confidence            544

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.32  E-value=1.9e-11  Score=125.38  Aligned_cols=174  Identities=25%  Similarity=0.324  Sum_probs=126.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|.++|..||.|..+.+..+..++.++|||||+|.+.++|..|+..++     +..|.|++|.|
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~-----~~~~~~~~~~v  189 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELN-----GKELEGRPLRV  189 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcC-----CCeECCceeEe
Confidence            5899999999999999999999999999999999998899999999999999999999999999     99999999999


Q ss_pred             EEccC----chhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCeE
Q 005812          505 LKALD----KKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRL  580 (676)
Q Consensus       505 ~~a~~----k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l  580 (676)
                      .++..    +......              ......                           ................+
T Consensus       190 ~~~~~~~~~~~~~~~~--------------~~~~~~---------------------------~~~~~~~~~~~~~~~~~  228 (306)
T COG0724         190 QKAQPASQPRSELSNN--------------LDASFA---------------------------KKLSRGKALLLEKSDNL  228 (306)
T ss_pred             eccccccccccccccc--------------cchhhh---------------------------cccccccccccccccee
Confidence            99764    1100000              000000                           00000001112234679


Q ss_pred             EEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCC
Q 005812          581 VIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPS  659 (676)
Q Consensus       581 ~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~  659 (676)
                      ++.|++..++..++...|.         .+|.+....+......      .......++.+.....+...+....++..
T Consensus       229 ~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  292 (306)
T COG0724         229 YVGNLPLKTAEEELADLFK---------SRGDIVRASLPPSKDG------KIPKSRSFVGNEASKDALESNSRGNKKKI  292 (306)
T ss_pred             eccccccccchhHHHHhcc---------ccccceeeeccCCCCC------cccccccccchhHHHhhhhhhccccceee
Confidence            9999999999999999999         5888876666544321      23444555666666666666666555433

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.31  E-value=7.2e-12  Score=121.24  Aligned_cols=77  Identities=22%  Similarity=0.323  Sum_probs=71.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      .++|||+|||+.+++++|+++|+.||.|.+|.|+.+..   ++|||||+|.++++|..||. |+|..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            56999999999999999999999999999999998753   57999999999999999996 999999999999999754


Q ss_pred             C
Q 005812          296 K  296 (676)
Q Consensus       296 ~  296 (676)
                      .
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            3

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.30  E-value=3.1e-12  Score=119.08  Aligned_cols=80  Identities=19%  Similarity=0.320  Sum_probs=73.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      .-++|||+||+|.+..+.|+++|++||.|++..|+.|+.+|+++|||||+|++.++|.+|++. -.-.|+||+-.|.++.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            457899999999999999999999999999999999999999999999999999999999995 4556899998888774


Q ss_pred             C
Q 005812          295 P  295 (676)
Q Consensus       295 ~  295 (676)
                      -
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            4

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.30  E-value=4.1e-13  Score=119.27  Aligned_cols=80  Identities=28%  Similarity=0.476  Sum_probs=76.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      +.-|||+|||+..||.||.-+|++||.|+.|.+++|+.+|.++||||++|++..+..-|+..||     |+.|.||.|+|
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~N-----Giki~gRtirV  109 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLN-----GIKILGRTIRV  109 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccC-----CceecceeEEe
Confidence            5789999999999999999999999999999999999999999999999999999999999999     99999999999


Q ss_pred             EEccC
Q 005812          505 LKALD  509 (676)
Q Consensus       505 ~~a~~  509 (676)
                      .....
T Consensus       110 DHv~~  114 (219)
T KOG0126|consen  110 DHVSN  114 (219)
T ss_pred             eeccc
Confidence            87554

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.30  E-value=5.4e-12  Score=106.46  Aligned_cols=87  Identities=25%  Similarity=0.524  Sum_probs=81.6

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEE
Q 005812          210 EGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIA  289 (676)
Q Consensus       210 ~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~  289 (676)
                      +......+.|||.++...++|++|.+.|..||.|..+.+..++.+|-.+|||+|+|.+.++|+.|+..+||..+-|..|.
T Consensus        66 PqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   66 PQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             CccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            44556789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCC
Q 005812          290 VDWAVPK  296 (676)
Q Consensus       290 v~~a~~~  296 (676)
                      |+|+-.+
T Consensus       146 VDw~Fv~  152 (170)
T KOG0130|consen  146 VDWCFVK  152 (170)
T ss_pred             EEEEEec
Confidence            9998543

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.29  E-value=5.5e-12  Score=106.41  Aligned_cols=86  Identities=23%  Similarity=0.350  Sum_probs=81.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ....+..|||.++...+++++|.+.|..||.|..+.+-.|..+|..+|||+|+|.+.++|+.|+..+|     |..|.|.
T Consensus        68 rSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~N-----g~~ll~q  142 (170)
T KOG0130|consen   68 RSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALN-----GAELLGQ  142 (170)
T ss_pred             cceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhcc-----chhhhCC
Confidence            45568999999999999999999999999999999999999999999999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.|+..+.
T Consensus       143 ~v~VDw~Fv~g  153 (170)
T KOG0130|consen  143 NVSVDWCFVKG  153 (170)
T ss_pred             ceeEEEEEecC
Confidence            99999988654

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.28  E-value=1.5e-11  Score=117.95  Aligned_cols=81  Identities=23%  Similarity=0.461  Sum_probs=77.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .+-+||||.-|+++++|.+|+..|+.||.|..|.|+.++.+|+++|||||+|+++-+...|.+..+     |.+|+|+.|
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~ad-----G~~Idgrri  173 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDAD-----GIKIDGRRI  173 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhcc-----CceecCcEE
Confidence            456899999999999999999999999999999999999999999999999999999999999999     999999999


Q ss_pred             EEEEcc
Q 005812          503 TVLKAL  508 (676)
Q Consensus       503 ~v~~a~  508 (676)
                      .|.+-.
T Consensus       174 ~VDvER  179 (335)
T KOG0113|consen  174 LVDVER  179 (335)
T ss_pred             EEEecc
Confidence            999844

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.28  E-value=7.1e-12  Score=113.72  Aligned_cols=81  Identities=23%  Similarity=0.390  Sum_probs=77.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      .-.+|.|-||-+.++.++|+.+|++||.|-.|.|+.|..++.++|||||.|-...+|+.|+++|+     |.+|+|+.|.
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damD-----G~~ldgRelr   86 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMD-----GAVLDGRELR   86 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhc-----ceeeccceee
Confidence            34789999999999999999999999999999999999999999999999999999999999999     9999999999


Q ss_pred             EEEccC
Q 005812          504 VLKALD  509 (676)
Q Consensus       504 v~~a~~  509 (676)
                      |++|.-
T Consensus        87 Vq~ary   92 (256)
T KOG4207|consen   87 VQMARY   92 (256)
T ss_pred             ehhhhc
Confidence            998763

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.28  E-value=7.6e-13  Score=117.56  Aligned_cols=80  Identities=29%  Similarity=0.448  Sum_probs=76.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      .+..|||+|||+..||.||.-.|++||.|.+|.+++|..||+++||||+.|++..+...|+..|||..|.||.|+|+...
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999998754

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.26  E-value=7.9e-12  Score=113.42  Aligned_cols=85  Identities=32%  Similarity=0.526  Sum_probs=79.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      ........|.|-||-+-++.++|+.+|++||.|-+|.|+.|+.++.++|||||.|....+|+.|+.+|+|..++|+.|.|
T Consensus         8 Pdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrV   87 (256)
T KOG4207|consen    8 PDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRV   87 (256)
T ss_pred             CCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeee
Confidence            34456689999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecC
Q 005812          291 DWAVP  295 (676)
Q Consensus       291 ~~a~~  295 (676)
                      +++.-
T Consensus        88 q~ary   92 (256)
T KOG4207|consen   88 QMARY   92 (256)
T ss_pred             hhhhc
Confidence            98753

>PLN03213 repressor of silencing 3; Provisional

Probab=99.25  E-value=2.6e-11  Score=123.21  Aligned_cols=78  Identities=19%  Similarity=0.258  Sum_probs=72.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCH--HHHHHHHHHcCCCCCCCeeecCcE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTV--EAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~--~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      .+.+|||+||++.++++||..+|+.||.|..|.|++  .+|  +|||||+|.+.  .++.+|+..||     |..+.||.
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLN-----GAEWKGR~   79 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYN-----GCVWKGGR   79 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhc-----CCeecCce
Confidence            457999999999999999999999999999999984  356  99999999988  78999999999     99999999


Q ss_pred             EEEEEccCc
Q 005812          502 LTVLKALDK  510 (676)
Q Consensus       502 l~v~~a~~k  510 (676)
                      |+|..|++.
T Consensus        80 LKVNKAKP~   88 (759)
T PLN03213         80 LRLEKAKEH   88 (759)
T ss_pred             eEEeeccHH
Confidence            999999874

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.24  E-value=2.2e-11  Score=116.83  Aligned_cols=83  Identities=23%  Similarity=0.396  Sum_probs=78.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ..+-+||||.-|+++++|..|+..|+.||.|..|.|+.+..+|+++|||||+|.++-+...|.+..+|..|+|+.|.|++
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ecC
Q 005812          293 AVP  295 (676)
Q Consensus       293 a~~  295 (676)
                      -.-
T Consensus       178 ERg  180 (335)
T KOG0113|consen  178 ERG  180 (335)
T ss_pred             ccc
Confidence            533

>smart00362 RRM_2 RNA recognition motif

Probab=99.24  E-value=4.9e-11  Score=94.44  Aligned_cols=72  Identities=38%  Similarity=0.565  Sum_probs=66.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       427 ~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      +|+|+|||..+++++|+++|..||.|..+.++.+.  +.++|+|||+|.+.++|.+|+..++     +..+.|+.|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~-----~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALN-----GTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhC-----CcEECCEEEeeC
Confidence            48999999999999999999999999999888765  6788999999999999999999999     999999999873

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.24  E-value=5.1e-11  Score=96.02  Aligned_cols=83  Identities=28%  Similarity=0.467  Sum_probs=75.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .+.-++.|||+|||+.+|.++..++|.+||.|..|+|-..+.   .+|-|||.|++..+|++|+.+|+|..++++.+.|-
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vl   90 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVL   90 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEE
Confidence            344578999999999999999999999999999999977543   67899999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      +..+..
T Consensus        91 yyq~~~   96 (124)
T KOG0114|consen   91 YYQPED   96 (124)
T ss_pred             ecCHHH
Confidence            987754

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.24  E-value=4.7e-11  Score=113.55  Aligned_cols=76  Identities=18%  Similarity=0.174  Sum_probs=70.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      +.+|||+||++.+|+++|+++|+.||.|.+|.|+++.   ..+++|||+|.++++|..|+ .|+     |..|.|++|.|
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLn-----Ga~l~d~~I~I   75 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLS-----GATIVDQRVCI   75 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcC-----CCeeCCceEEE
Confidence            5799999999999999999999999999999999873   45689999999999999999 799     99999999999


Q ss_pred             EEccC
Q 005812          505 LKALD  509 (676)
Q Consensus       505 ~~a~~  509 (676)
                      ..+..
T Consensus        76 t~~~~   80 (243)
T PLN03121         76 TRWGQ   80 (243)
T ss_pred             EeCcc
Confidence            98654

>PLN03213 repressor of silencing 3; Provisional

Probab=99.23  E-value=2.2e-11  Score=123.73  Aligned_cols=79  Identities=18%  Similarity=0.315  Sum_probs=72.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCH--HHHHHHHHHhCCceeCCeeEEEE
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK--RDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~--~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      ....+|||+||++.+++++|+.+|..||.|.+|.|++  .+|  +|||||+|.+.  .++.+||..|||..+.|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            3457999999999999999999999999999999994  466  89999999987  78999999999999999999999


Q ss_pred             EecCC
Q 005812          292 WAVPK  296 (676)
Q Consensus       292 ~a~~~  296 (676)
                      .++|.
T Consensus        84 KAKP~   88 (759)
T PLN03213         84 KAKEH   88 (759)
T ss_pred             eccHH
Confidence            88764

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.23  E-value=8.7e-12  Score=113.97  Aligned_cols=88  Identities=27%  Similarity=0.437  Sum_probs=83.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||++|...++|.-|...|=+||.|..|.++.|.++++.+|||||+|.-.++|..||..||+..+.|+.|+|.+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 005812          293 AVPKNIYS  300 (676)
Q Consensus       293 a~~~~~~~  300 (676)
                      +.|.....
T Consensus        87 AkP~kike   94 (298)
T KOG0111|consen   87 AKPEKIKE   94 (298)
T ss_pred             cCCccccC
Confidence            99876543

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.23  E-value=3.7e-11  Score=106.60  Aligned_cols=77  Identities=22%  Similarity=0.336  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      ..+.|||+||+..+++.||...|..||.|.+|.|-..     +.|||||+|+++.+|..|+..|+     |..|.|..|.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LD-----G~~~cG~r~r   78 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLD-----GKDICGSRIR   78 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcC-----CccccCceEE
Confidence            3589999999999999999999999999999987654     58999999999999999999999     9999999999


Q ss_pred             EEEccCc
Q 005812          504 VLKALDK  510 (676)
Q Consensus       504 v~~a~~k  510 (676)
                      |+++.-+
T Consensus        79 VE~S~G~   85 (195)
T KOG0107|consen   79 VELSTGR   85 (195)
T ss_pred             EEeecCC
Confidence            9997644

>smart00360 RRM RNA recognition motif

Probab=99.21  E-value=6.1e-11  Score=93.56  Aligned_cols=71  Identities=38%  Similarity=0.550  Sum_probs=66.6

Q ss_pred             EcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          430 ICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       430 V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      |+|||..+++++|+++|+.||.|..+.+..+..++.++|+|||+|.+.++|.+|+..++     +..++|+.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~-----~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALN-----GKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcC-----CCeeCCcEEEeC
Confidence            57999999999999999999999999998887778899999999999999999999999     999999999873

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.20  E-value=6.9e-11  Score=112.41  Aligned_cols=76  Identities=20%  Similarity=0.231  Sum_probs=69.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ...+|||+||++.+|+++|+++|+.||.|.+|.|+++.   ..++||||+|.++++|..|+. |+|..|.++.|.|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            45799999999999999999999999999999999874   456899999999999999997 89999999999998764

>smart00362 RRM_2 RNA recognition motif

Probab=99.20  E-value=7.4e-11  Score=93.43  Aligned_cols=71  Identities=45%  Similarity=0.789  Sum_probs=66.7

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       218 ~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      +|+|+|||..++.++|+++|..||.|..+.+..++  +.++|+|||+|.+.++|+.|+..+++..+.|+.|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            48999999999999999999999999999998875  678899999999999999999999999999999887

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=99.18  E-value=1.1e-12  Score=142.13  Aligned_cols=233  Identities=19%  Similarity=0.139  Sum_probs=179.6

Q ss_pred             CcEEEEcCCCccccH-HHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecC
Q 005812          121 ARTVIIGGLLNADMA-EEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKG  199 (676)
Q Consensus       121 ~~~l~V~nLp~~~~~-~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~  199 (676)
                      .+...+.++.+.... +..+..|+.+|.|..++++.-.         ..-.....+++.+....+++.|.. ..+..+.+
T Consensus       571 ~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g---------~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~  640 (881)
T KOG0128|consen  571 RREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRG---------FKAHEQPQQQKVQSKHGSAESATV-PAGGALAN  640 (881)
T ss_pred             hhhhcccCCCcchhhHHhhHHHhhcccccccccCcccc---------ccccccchhhhhhccccchhhccc-ccccccCC
Confidence            344566666555543 3678899999999999976411         111223367899999999988865 56666777


Q ss_pred             eEEEEecCCCCC----------CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHH
Q 005812          200 GTVWARQLGGEG----------SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKR  269 (676)
Q Consensus       200 ~~i~v~~~~~~~----------~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~  269 (676)
                      +...+-......          ......++||+||+..+.+.+|...|..+|.+..+++.-....+..+|+|||.|..++
T Consensus       641 ~~~av~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~  720 (881)
T KOG0128|consen  641 RSAAVGLADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPE  720 (881)
T ss_pred             ccccCCCCCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCC
Confidence            666553322111          1123478999999999999999999999999988877755567889999999999999


Q ss_pred             HHHHHHHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCC
Q 005812          270 DAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNAD  349 (676)
Q Consensus       270 ~A~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  349 (676)
                      +|.+|+....+.. .|          +                                                     
T Consensus       721 ~~~aaV~f~d~~~-~g----------K-----------------------------------------------------  736 (881)
T KOG0128|consen  721 HAGAAVAFRDSCF-FG----------K-----------------------------------------------------  736 (881)
T ss_pred             chhhhhhhhhhhh-hh----------h-----------------------------------------------------
Confidence            9999999533322 22          0                                                     


Q ss_pred             chhHHHHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEE
Q 005812          350 FDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIF  429 (676)
Q Consensus       350 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  429 (676)
                                                                                                  ..|+
T Consensus       737 ----------------------------------------------------------------------------~~v~  740 (881)
T KOG0128|consen  737 ----------------------------------------------------------------------------ISVA  740 (881)
T ss_pred             ----------------------------------------------------------------------------hhhh
Confidence                                                                                        3699


Q ss_pred             EcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccC
Q 005812          430 ICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALD  509 (676)
Q Consensus       430 V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~  509 (676)
                      |.|.|+..|.++++.+|+++|++.+++++.. ..|+++|.|+|.|.++.+|.+++..+.     ...+.-+.+.|..+.+
T Consensus       741 i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~-r~gkpkg~a~v~y~~ea~~s~~~~s~d-----~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  741 ISGPPFQGTKEELKSLASKTGNVTSLRLVTV-RAGKPKGKARVDYNTEADASRKVASVD-----VAGKRENNGEVQVSNP  814 (881)
T ss_pred             eeCCCCCCchHHHHhhccccCCccccchhhh-hccccccceeccCCCcchhhhhcccch-----hhhhhhcCccccccCC
Confidence            9999999999999999999999999987666 468999999999999999999999888     7777777777766554

>smart00360 RRM RNA recognition motif

Probab=99.16  E-value=1e-10  Score=92.31  Aligned_cols=71  Identities=38%  Similarity=0.707  Sum_probs=66.6

Q ss_pred             EcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       221 V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      |+|||..+++++|+.+|..||.|..+.+..++.++.++|+|||+|.+.++|..|+..+++..+.|+.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57999999999999999999999999999887778899999999999999999999999999999998873

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.15  E-value=2.1e-11  Score=111.50  Aligned_cols=82  Identities=24%  Similarity=0.408  Sum_probs=79.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||++|..++++.-|...|-+||.|..|.++.|-.+++.+|||||+|...++|..|+..||     +..|.||.|+|
T Consensus        10 KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMn-----esEL~GrtirV   84 (298)
T KOG0111|consen   10 KRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMN-----ESELFGRTIRV   84 (298)
T ss_pred             ceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCc-----hhhhcceeEEE
Confidence            3799999999999999999999999999999999999999999999999999999999999999     99999999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .+|.|..
T Consensus        85 N~AkP~k   91 (298)
T KOG0111|consen   85 NLAKPEK   91 (298)
T ss_pred             eecCCcc
Confidence            9999854

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.15  E-value=3.3e-10  Score=90.18  Aligned_cols=74  Identities=39%  Similarity=0.551  Sum_probs=68.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEE
Q 005812          427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLK  506 (676)
Q Consensus       427 ~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~  506 (676)
                      +|+|+|||..+++++|+++|+.||.|..+.+..+... .++|+|||+|.+.++|..|+..++     +..+.|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~-----~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALN-----GKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhC-----CCeECCeEEEEeC
Confidence            4899999999999999999999999999988877544 679999999999999999999999     8999999999864

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=99.12  E-value=9.1e-12  Score=135.16  Aligned_cols=199  Identities=19%  Similarity=0.142  Sum_probs=161.9

Q ss_pred             eEEEEecCHHHHHHHHHHhCCceecCeEEEEeeccccchHHHhhhhhchhhhhhhhhhccCCCCCcccccccccchhhcc
Q 005812           13 FGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAEDIEKTMDNKDGVISGAEKHSSKLLES   92 (676)
Q Consensus        13 ~afV~F~~~edA~~Al~~~~g~~i~gr~i~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (676)
                      ++++.+....+++.|... .|.-+.++.+.|..+.+++...                                       
T Consensus       616 ~~~~~~s~~~~~esat~p-a~~~~a~~~~av~~ad~~~~~~---------------------------------------  655 (881)
T KOG0128|consen  616 QQQKVQSKHGSAESATVP-AGGALANRSAAVGLADAEEKEE---------------------------------------  655 (881)
T ss_pred             hhhhhhccccchhhcccc-cccccCCccccCCCCCchhhhh---------------------------------------
Confidence            889999999999999887 8889999999998886553111                                       


Q ss_pred             CCCCCCCcccccCcccCCCCccchhcccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCcc
Q 005812           93 GKTVKPRKAATLGIDLADKEDCSQKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKM  172 (676)
Q Consensus        93 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~  172 (676)
                                       +........+...++||+||+..+.+.+|+..|..+|.+..+.+..-+         ..++.+
T Consensus       656 -----------------~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~---------n~~~~r  709 (881)
T KOG0128|consen  656 -----------------NFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHK---------NEKRFR  709 (881)
T ss_pred             -----------------ccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHh---------hccccc
Confidence                             000011122445678999999999999999999999988877754222         347889


Q ss_pred             ceEEEEeCCHHHHHHHHHHhCCCeecCeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccC
Q 005812          173 DASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNT  252 (676)
Q Consensus       173 g~afV~F~~~~~A~~A~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~  252 (676)
                      |+||+.|..++++.+|+....+..++                 +..|+|+|+|+..|.++++.+++.+|.+.+++++..+
T Consensus       710 G~~Y~~F~~~~~~~aaV~f~d~~~~g-----------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r  772 (881)
T KOG0128|consen  710 GKAYVEFLKPEHAGAAVAFRDSCFFG-----------------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR  772 (881)
T ss_pred             cceeeEeecCCchhhhhhhhhhhhhh-----------------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh
Confidence            99999999999999999955544333                 4579999999999999999999999999999988764


Q ss_pred             CCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          253 DTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       253 ~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                       .|+.+|.|||.|.++.+|.+++...+...+.-+.+.|..+.|
T Consensus       773 -~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  773 -AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             -ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence             789999999999999999999998888888778888887766

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.12  E-value=1.4e-10  Score=121.92  Aligned_cols=85  Identities=34%  Similarity=0.548  Sum_probs=80.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      +.|||+|+|+++++++|.++|+..|.|.+++++.|..+|+++||||++|.+.++|.+|++.||     |..+.||+|+|.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lN-----g~~~~gr~l~v~   93 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLN-----GAEFNGRKLRVN   93 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcC-----CcccCCceEEee
Confidence            799999999999999999999999999999999999999999999999999999999999999     999999999999


Q ss_pred             EccCchhhhh
Q 005812          506 KALDKKLAHD  515 (676)
Q Consensus       506 ~a~~k~~~~~  515 (676)
                      |+...+....
T Consensus        94 ~~~~~~~~~~  103 (435)
T KOG0108|consen   94 YASNRKNAER  103 (435)
T ss_pred             cccccchhHH
Confidence            9887665443

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.11  E-value=5e-10  Score=89.10  Aligned_cols=74  Identities=39%  Similarity=0.714  Sum_probs=68.3

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       218 ~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      +|+|+|||..+++++|+++|..||.|..+.+..++.+ ..+|+|||+|.+.++|..|++.+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999987644 5789999999999999999999999999999999864

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.08  E-value=2.2e-10  Score=120.45  Aligned_cols=81  Identities=32%  Similarity=0.593  Sum_probs=78.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      +.|||+|+|+++++++|..+|+..|.|.+++++.|+.+|+.+||||++|.+.++|..|++.|||..+.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999998654


Q ss_pred             C
Q 005812          297 N  297 (676)
Q Consensus       297 ~  297 (676)
                      .
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            3

>smart00361 RRM_1 RNA recognition motif

Probab=99.08  E-value=4.9e-10  Score=88.49  Aligned_cols=61  Identities=26%  Similarity=0.511  Sum_probs=55.6

Q ss_pred             HHHHHHHHH----hCCceeEEE-EeecCCC--CCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          439 NEEVKQRFS----AFGEVVSFV-PVLHQVT--KRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       439 eedl~~~F~----~~G~v~~v~-i~~~~~~--~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      +++|+++|+    +||.|.++. ++.++.+  +.++|||||+|.+.++|.+|+..||     |..+.||.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~-----g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLN-----GRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhC-----CCEECCEEEEe
Confidence            578899998    999999995 7777666  8899999999999999999999999     99999999986

>PF13893 RRM_5: RNA recognition motif

Probab=99.07  E-value=6.6e-10  Score=83.60  Aligned_cols=56  Identities=39%  Similarity=0.726  Sum_probs=51.1

Q ss_pred             HHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          233 IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       233 l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      |+++|++||.|.++.+..+.     +++|||+|.+.++|+.|++.|||..+.|++|+|.||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68899999999999998752     589999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>PF13893 RRM_5: RNA recognition motif

Probab=99.06  E-value=6e-10  Score=83.82  Aligned_cols=56  Identities=34%  Similarity=0.497  Sum_probs=50.2

Q ss_pred             HHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEc
Q 005812          442 VKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA  507 (676)
Q Consensus       442 l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a  507 (676)
                      |+++|++||.|..+.+....     +++|||+|.+.++|..|++.||     |..++|++|.|.||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~-----~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLN-----GRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHT-----TSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhC-----CCEECCcEEEEEEC
Confidence            68999999999999876442     6899999999999999999999     99999999999985

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>smart00361 RRM_1 RNA recognition motif

Probab=99.01  E-value=1.2e-09  Score=86.28  Aligned_cols=61  Identities=25%  Similarity=0.362  Sum_probs=54.7

Q ss_pred             HHHHHHhhc----cCCceEEEE-EcccCCC--CCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          230 VNEIKDMFS----PVGLVWNVY-IPHNTDT--GLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       230 e~~l~~~F~----~~G~i~~v~-i~~~~~~--~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      +++|+++|+    .||.|.++. ++.++.+  +.++|||||+|.+.++|.+|++.|||..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578888898    999999995 6666555  889999999999999999999999999999999976

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.01  E-value=8.6e-09  Score=106.84  Aligned_cols=172  Identities=24%  Similarity=0.309  Sum_probs=119.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCC---CCcee---EEEEEecCHHHHHHHHHHhCCceeC
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDT---GLSKG---FAFVKFTCKRDAESAIQKFNGQKFG  284 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~---~~~~g---~afV~f~~~~~A~~A~~~l~~~~~~  284 (676)
                      ....-.+.|||++||++++|++|...|..||.+. |.++.....   -..+|   |+|+-|+++...+.-+....-   +
T Consensus       254 ~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~---~  329 (520)
T KOG0129|consen  254 RSPRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE---G  329 (520)
T ss_pred             CccccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh---c
Confidence            3445578999999999999999999999999876 666642211   13455   999999999998887765432   4


Q ss_pred             CeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcc
Q 005812          285 KRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKL  364 (676)
Q Consensus       285 g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  364 (676)
                      ...+.+..+.+......      .+-......                              +..|-.            
T Consensus       330 ~~~~yf~vss~~~k~k~------VQIrPW~la------------------------------Ds~fv~------------  361 (520)
T KOG0129|consen  330 EGNYYFKVSSPTIKDKE------VQIRPWVLA------------------------------DSDFVL------------  361 (520)
T ss_pred             ccceEEEEecCcccccc------eeEEeeEec------------------------------cchhhh------------
Confidence            44444444433211000      000000000                              000000            


Q ss_pred             cccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHH
Q 005812          365 TSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQ  444 (676)
Q Consensus       365 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~  444 (676)
                                                                          .......+.+||||++||-.++.++|..
T Consensus       362 ----------------------------------------------------d~sq~lDprrTVFVGgvprpl~A~eLA~  389 (520)
T KOG0129|consen  362 ----------------------------------------------------DHNQPIDPRRTVFVGGLPRPLTAEELAM  389 (520)
T ss_pred             ----------------------------------------------------ccCcccCccceEEecCCCCcchHHHHHH
Confidence                                                                0000223458999999999999999999


Q ss_pred             HHH-hCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 005812          445 RFS-AFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA  486 (676)
Q Consensus       445 ~F~-~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~  486 (676)
                      +|. -||.|.++-|-.|++-+.++|-|-|+|.+..+-.+||.+
T Consensus       390 imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  390 IMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             HHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            999 699999999999987889999999999999999999976

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.00  E-value=6.9e-10  Score=108.65  Aligned_cols=85  Identities=21%  Similarity=0.349  Sum_probs=80.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      .+|.+.|||+-|.+-++++||.-+|+.||.|.+|.|++|..+|.+..||||+|.+.+++.+|.-+|+     +..|++|.
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMd-----NvLIDDrR  310 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMD-----NVLIDDRR  310 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhc-----ceeeccce
Confidence            3456899999999999999999999999999999999999999999999999999999999999999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |+|.|+++-.
T Consensus       311 IHVDFSQSVs  320 (479)
T KOG0415|consen  311 IHVDFSQSVS  320 (479)
T ss_pred             EEeehhhhhh
Confidence            9999987643

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.97  E-value=3.6e-09  Score=87.41  Aligned_cols=84  Identities=23%  Similarity=0.263  Sum_probs=75.7

Q ss_pred             CCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcC
Q 005812          577 RTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN  656 (676)
Q Consensus       577 ~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng  656 (676)
                      +|+|+|||||...|.++|.+++.+.       -.|...-+.++.|..+.      -+.|||||.|.+++.|.+-.+.++|
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~-------~~g~yDF~YLPiDf~~~------~N~GYAFVNf~~~~~~~~F~~~f~g   67 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEH-------FKGKYDFFYLPIDFKNK------CNLGYAFVNFTSPQAAIRFYKAFNG   67 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHh-------ccCcceEEEeeeeccCC------CceEEEEEEcCCHHHHHHHHHHHcC
Confidence            3799999999999999999999975       25778889999998775      7899999999999999999999999


Q ss_pred             CCC-CCCcccCccccccc
Q 005812          657 NPS-KLFYHHCFDAADAQ  673 (676)
Q Consensus       657 ~~~-~~~~~~~~~~~~~~  673 (676)
                      .+| .|...+.+.|+||.
T Consensus        68 ~~w~~~~s~Kvc~i~yAr   85 (97)
T PF04059_consen   68 KKWPNFNSKKVCEISYAR   85 (97)
T ss_pred             CccccCCCCcEEEEehhH
Confidence            999 68889999999985

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.96  E-value=1.2e-08  Score=105.78  Aligned_cols=157  Identities=20%  Similarity=0.244  Sum_probs=116.4

Q ss_pred             hcccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCC--
Q 005812          117 KQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQ--  194 (676)
Q Consensus       117 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~--  194 (676)
                      ..+.++.||||+||++++|+.|...|..||.+. |..+.....   .+.....-+-||+|+.|+++..++.-+..+.-  
T Consensus       255 ~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~---~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~  330 (520)
T KOG0129|consen  255 SPRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANS---RGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGE  330 (520)
T ss_pred             ccccccceeecCCCccccHHHHHhhcccccceE-eecCCCccc---cccCCCCCcccEEEEEecchHHHHHHHHHHhhcc
Confidence            346788999999999999999999999999753 344431110   00111111225999999999999988876532  


Q ss_pred             ---------CeecCeEEEEec---------CCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhc-cCCceEEEEEcccCCCC
Q 005812          195 ---------KEIKGGTVWARQ---------LGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFS-PVGLVWNVYIPHNTDTG  255 (676)
Q Consensus       195 ---------~~~~~~~i~v~~---------~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~-~~G~i~~v~i~~~~~~~  255 (676)
                               ..+..+.+.+++         ..........+||||++||.-++.++|..+|+ -||.|..+-|-.|++-+
T Consensus       331 ~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~K  410 (520)
T KOG0129|consen  331 GNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLK  410 (520)
T ss_pred             cceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccC
Confidence                     111222222221         11223445679999999999999999999999 59999999999998888


Q ss_pred             CceeEEEEEecCHHHHHHHHHH
Q 005812          256 LSKGFAFVKFTCKRDAESAIQK  277 (676)
Q Consensus       256 ~~~g~afV~f~~~~~A~~A~~~  277 (676)
                      -.+|-|-|.|.+..+--+||.+
T Consensus       411 YPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  411 YPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CCCCcceeeecccHHHHHHHhh
Confidence            8999999999999999999985

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.86  E-value=2.9e-09  Score=104.33  Aligned_cols=87  Identities=22%  Similarity=0.297  Sum_probs=81.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      ..++...|||..|.+.++.++|.-+|+.||.|.+|.|+++..+|.+-.||||+|.+.+++++|.-+|++..|..++|+|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            45677899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.+-..
T Consensus       315 FSQSVsk  321 (479)
T KOG0415|consen  315 FSQSVSK  321 (479)
T ss_pred             hhhhhhh
Confidence            9866443

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.83  E-value=1e-09  Score=100.77  Aligned_cols=139  Identities=18%  Similarity=0.263  Sum_probs=119.5

Q ss_pred             cCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecC
Q 005812          120 VARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKG  199 (676)
Q Consensus       120 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~  199 (676)
                      ..+||||+|+...++++-|.++|-+.|+|..|.|+.+++          +..+ ||||.|.++-.+.-|+.-+||..+.+
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d----------~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~   76 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD----------QEQK-FAYVFFPNENSVQLAGQLENGDDLEE   76 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc----------CCCc-eeeeecccccchhhhhhhcccchhcc
Confidence            457999999999999999999999999999999987654          5555 99999999999999999999999998


Q ss_pred             eEEEEecCCCCCCCCCCcEEEEcC----CCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHH
Q 005812          200 GTVWARQLGGEGSKTQKWKLIIRN----IPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI  275 (676)
Q Consensus       200 ~~i~v~~~~~~~~~~~~~~v~V~n----Lp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~  275 (676)
                      ..+.+.             ++-++    |...++++.+...|+.-|++..+++.++. +|+++.++|+.+-...+.-.++
T Consensus        77 ~e~q~~-------------~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~-d~rnrn~~~~~~qr~~~~P~~~  142 (267)
T KOG4454|consen   77 DEEQRT-------------LRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDN-DGRNRNFGFVTYQRLCAVPFAL  142 (267)
T ss_pred             chhhcc-------------cccCCCcchhhhhcchhhheeeecccCCCCCccccccc-cCCccCccchhhhhhhcCcHHh
Confidence            888774             44455    66778999999999999999999999885 5888899999988877777788


Q ss_pred             HHhCCcee
Q 005812          276 QKFNGQKF  283 (676)
Q Consensus       276 ~~l~~~~~  283 (676)
                      ....+...
T Consensus       143 ~~y~~l~~  150 (267)
T KOG4454|consen  143 DLYQGLEL  150 (267)
T ss_pred             hhhcccCc
Confidence            76666544

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.80  E-value=1.7e-08  Score=92.69  Aligned_cols=82  Identities=21%  Similarity=0.353  Sum_probs=75.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhC-CceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAF-GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~-G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      ....++|..+|..+.+.++..+|.+| |.|..+++-+++.+|.++|||||+|++++.|.-|-..||     +..|.|+.|
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMN-----NYLl~e~lL  122 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMN-----NYLLMEHLL  122 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhh-----hhhhhhhee
Confidence            34589999999999999999999998 778888888999999999999999999999999999999     999999999


Q ss_pred             EEEEccCc
Q 005812          503 TVLKALDK  510 (676)
Q Consensus       503 ~v~~a~~k  510 (676)
                      .|.+-.+-
T Consensus       123 ~c~vmppe  130 (214)
T KOG4208|consen  123 ECHVMPPE  130 (214)
T ss_pred             eeEEeCch
Confidence            99885543

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.79  E-value=1.9e-08  Score=92.36  Aligned_cols=85  Identities=25%  Similarity=0.331  Sum_probs=78.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccC-CceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPV-GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~-G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      .......++|..+|..+.+.++..+|.++ |.|..+++.+++.||.++|||||+|.+++.|.-|-+.||+..|.++.|.|
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            34456789999999999999999999998 77888899899999999999999999999999999999999999999999


Q ss_pred             EEecCC
Q 005812          291 DWAVPK  296 (676)
Q Consensus       291 ~~a~~~  296 (676)
                      .+..|.
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            998765

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.79  E-value=4.9e-09  Score=105.58  Aligned_cols=178  Identities=18%  Similarity=0.225  Sum_probs=140.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCc-eeCCeeEEEEE
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQ-KFGKRPIAVDW  292 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~-~~~g~~i~v~~  292 (676)
                      ...++.|++++...+.+.+...++..+|....+.+........++|++++.|...+.+..|+.. .+. .+.++.+....
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~-s~~~~~~~~~~~~dl  164 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEE-SGSKVLDGNKGEKDL  164 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHh-hhccccccccccCcc
Confidence            3567899999999999998999999999888887777666788999999999999999999995 553 45555555444


Q ss_pred             ecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCC
Q 005812          293 AVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLP  372 (676)
Q Consensus       293 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  372 (676)
                      ......+.....                                                                    
T Consensus       165 ~~~~~~~~~n~~--------------------------------------------------------------------  176 (285)
T KOG4210|consen  165 NTRRGLRPKNKL--------------------------------------------------------------------  176 (285)
T ss_pred             cccccccccchh--------------------------------------------------------------------
Confidence            332221000000                                                                    


Q ss_pred             CCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEE-EcCCCCCCCHHHHHHHHHhCCc
Q 005812          373 SLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIF-ICNLPFDLDNEEVKQRFSAFGE  451 (676)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-V~nLp~~~teedl~~~F~~~G~  451 (676)
                                                                  .. .......++| +.||++.+++++|+.+|..+|.
T Consensus       177 --------------------------------------------~~-~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~  211 (285)
T KOG4210|consen  177 --------------------------------------------SR-LSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGE  211 (285)
T ss_pred             --------------------------------------------cc-cccCccccceeecccccccchHHHhhhccCcCc
Confidence                                                        00 0111123444 9999999999999999999999


Q ss_pred             eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCch
Q 005812          452 VVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       452 v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~  511 (676)
                      |..++++.+..++.++|||||.|.....+..++.. .     ...+.++++.+.+..++.
T Consensus       212 i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~-----~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  212 ITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-Q-----TRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             ceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-c-----cCcccCcccccccCCCCc
Confidence            99999999999999999999999999999999987 7     889999999999987764

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.77  E-value=4.4e-09  Score=115.13  Aligned_cols=163  Identities=18%  Similarity=0.197  Sum_probs=137.8

Q ss_pred             hcccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCe
Q 005812          117 KQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKE  196 (676)
Q Consensus       117 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~  196 (676)
                      ..+..++||++||+..+++.+|+..|..+|.|.+|.+-..+          -+....||||.|.+...+-.|...+.+..
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~----------~~~esa~~f~~~~n~dmtp~ak~e~s~~~  437 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH----------IKTESAYAFVSLLNTDMTPSAKFEESGPL  437 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC----------CCcccchhhhhhhccccCcccchhhcCCc
Confidence            44678899999999999999999999999999999865432          35667889999999999999999999988


Q ss_pred             ecCeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHH
Q 005812          197 IKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ  276 (676)
Q Consensus       197 ~~~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~  276 (676)
                      |....+.+.-..  ......+.+++++|+..+....|...|..||.|..|.+-.      ..-||||.|.+...|+.|++
T Consensus       438 I~~g~~r~glG~--~kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h------gq~yayi~yes~~~aq~a~~  509 (975)
T KOG0112|consen  438 IGNGTHRIGLGQ--PKSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH------GQPYAYIQYESPPAAQAATH  509 (975)
T ss_pred             cccCcccccccc--cccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc------CCcceeeecccCccchhhHH
Confidence            887765553221  2556778999999999999999999999999999876644      44699999999999999999


Q ss_pred             HhCCceeCC--eeEEEEEecCCC
Q 005812          277 KFNGQKFGK--RPIAVDWAVPKN  297 (676)
Q Consensus       277 ~l~~~~~~g--~~i~v~~a~~~~  297 (676)
                      .|.|..|++  +.+.|.++.+..
T Consensus       510 ~~rgap~G~P~~r~rvdla~~~~  532 (975)
T KOG0112|consen  510 DMRGAPLGGPPRRLRVDLASPPG  532 (975)
T ss_pred             HHhcCcCCCCCcccccccccCCC
Confidence            999999975  779999986643

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.73  E-value=1e-08  Score=96.63  Aligned_cols=81  Identities=20%  Similarity=0.324  Sum_probs=75.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      ..||.+.|--+++++-|-..|.+|-.....++++++.+|+++||+||.|.++.++.+|+..|+     |..++.|+|.+.
T Consensus       191 fRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~-----gkyVgsrpiklR  265 (290)
T KOG0226|consen  191 FRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMN-----GKYVGSRPIKLR  265 (290)
T ss_pred             ceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhc-----ccccccchhHhh
Confidence            589999999999999999999999999999999999999999999999999999999999999     999999999987


Q ss_pred             EccCch
Q 005812          506 KALDKK  511 (676)
Q Consensus       506 ~a~~k~  511 (676)
                      ....++
T Consensus       266 kS~wke  271 (290)
T KOG0226|consen  266 KSEWKE  271 (290)
T ss_pred             hhhHHh
Confidence            655544

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.70  E-value=4.5e-08  Score=96.41  Aligned_cols=80  Identities=28%  Similarity=0.410  Sum_probs=70.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      .+..-.+|||++|-..+++.+|+++|.+||.|++++++..      +++|||+|.+.+.|..|..++-.    .+.|+|+
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n----~lvI~G~  293 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFN----KLVINGF  293 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcc----eeeecce
Confidence            4445689999999989999999999999999999988754      56999999999999999877641    6888999


Q ss_pred             EEEEEEccCc
Q 005812          501 QLTVLKALDK  510 (676)
Q Consensus       501 ~l~v~~a~~k  510 (676)
                      +|.|.|..++
T Consensus       294 Rl~i~Wg~~~  303 (377)
T KOG0153|consen  294 RLKIKWGRPK  303 (377)
T ss_pred             EEEEEeCCCc
Confidence            9999999884

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.69  E-value=1.8e-08  Score=101.46  Aligned_cols=169  Identities=18%  Similarity=0.270  Sum_probs=135.0

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeec
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIK  198 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~  198 (676)
                      ....++|++++...+.+.++..++..+|.+..+.+....         ....++|++++.|...+.+..|+...-...+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~---------~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~  156 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLE---------DSLSSKGGLSVHFAGKSQFFAALEESGSKVLD  156 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhc---------cccccccceeeccccHHHHHHHHHhhhccccc
Confidence            356789999999999999999999999988777755432         34788999999999999999999854333444


Q ss_pred             CeEEEE-----ecC-----CCCCCCCCCcEEE-EcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecC
Q 005812          199 GGTVWA-----RQL-----GGEGSKTQKWKLI-IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC  267 (676)
Q Consensus       199 ~~~i~v-----~~~-----~~~~~~~~~~~v~-V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~  267 (676)
                      +..+..     +..     ..........++| |++|+..+++++|+.+|..+|.|..++++.++.++..+|||||.|..
T Consensus       157 ~~~~~~dl~~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~  236 (285)
T KOG4210|consen  157 GNKGEKDLNTRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSA  236 (285)
T ss_pred             cccccCcccccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhh
Confidence            433321     110     0011222345555 99999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhCCceeCCeeEEEEEecCCC
Q 005812          268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKN  297 (676)
Q Consensus       268 ~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~  297 (676)
                      ...+..++.. ....+.++++.+....+..
T Consensus       237 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  237 GNSKKLALND-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             chhHHHHhhc-ccCcccCcccccccCCCCc
Confidence            9999999987 7888899999999887764

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.66  E-value=5.9e-09  Score=95.87  Aligned_cols=79  Identities=22%  Similarity=0.283  Sum_probs=70.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||.|+...++|+-|.++|-+-|+|..|.|+.++ ++..+ ||||.|.++....-|++-+||..+.++.+.|.
T Consensus         5 aae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~   82 (267)
T KOG4454|consen    5 AAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRT   82 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcc
Confidence            34456899999999999999999999999999999999876 45455 99999999999999999999999988888876


Q ss_pred             E
Q 005812          292 W  292 (676)
Q Consensus       292 ~  292 (676)
                      +
T Consensus        83 ~   83 (267)
T KOG4454|consen   83 L   83 (267)
T ss_pred             c
Confidence            4

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.60  E-value=8e-08  Score=103.75  Aligned_cols=78  Identities=19%  Similarity=0.433  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .-++||||++||..++++||.++|+.||.|.+|.++      .++|||||++....+|.+|+.+|+     ...+.++.|
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li------~~R~cAfI~M~~RqdA~kalqkl~-----n~kv~~k~I  487 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI------PPRGCAFIKMVRRQDAEKALQKLS-----NVKVADKTI  487 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeec------cCCceeEEEEeehhHHHHHHHHHh-----cccccceee
Confidence            347899999999999999999999999999999664      358999999999999999999999     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      +|.||..+.
T Consensus       488 ki~Wa~g~G  496 (894)
T KOG0132|consen  488 KIAWAVGKG  496 (894)
T ss_pred             EEeeeccCC
Confidence            999999875

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.59  E-value=3.9e-08  Score=92.75  Aligned_cols=162  Identities=13%  Similarity=0.111  Sum_probs=123.9

Q ss_pred             cEEEEcCCCccccHHH-H--HHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeec
Q 005812          122 RTVIIGGLLNADMAEE-V--HRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIK  198 (676)
Q Consensus       122 ~~l~V~nLp~~~~~~~-l--~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~  198 (676)
                      -..+++++-..+..+- |  ...|+.+-......+..+          +.+.-++++|+.|.....-.++-..-+++.+.
T Consensus        97 f~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~----------~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~  166 (290)
T KOG0226|consen   97 FRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRD----------RPQPIRPEAFESFKASDALLKAETEKEKKKIG  166 (290)
T ss_pred             ccccccccccccCCCCCCcchhhhccchhhhhhhhhhc----------CCCccCcccccCcchhhhhhhhcccccccccc
Confidence            3566666655554433 2  556666654444443332          34677899999999888888877766777776


Q ss_pred             CeEEEEecCC------CCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHH
Q 005812          199 GGTVWARQLG------GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAE  272 (676)
Q Consensus       199 ~~~i~v~~~~------~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~  272 (676)
                      -..++.....      -........+||.+.|...++.+-|-..|.+|-.....++++++.+|+++||+||.|.+..++.
T Consensus       167 ~~~VR~a~gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~  246 (290)
T KOG0226|consen  167 KPPVRLAAGTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYV  246 (290)
T ss_pred             CcceeeccccccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHH
Confidence            6655442211      1123456789999999999999999999999999889999999999999999999999999999


Q ss_pred             HHHHHhCCceeCCeeEEEEEe
Q 005812          273 SAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       273 ~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      +|+..|+|..++.+.|.+.-+
T Consensus       247 rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  247 RAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             HHHHhhcccccccchhHhhhh
Confidence            999999999999999988654

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.57  E-value=9.8e-08  Score=103.08  Aligned_cols=78  Identities=27%  Similarity=0.502  Sum_probs=72.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      -++||||++|+..+++.||..+|+.||.|.+|.++.      ++|+|||.+.+..+|.+|+.+|+...+.++.|+|.|+.
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            368999999999999999999999999999999887      67999999999999999999999999999999999997


Q ss_pred             CCCC
Q 005812          295 PKNI  298 (676)
Q Consensus       295 ~~~~  298 (676)
                      .+..
T Consensus       494 g~G~  497 (894)
T KOG0132|consen  494 GKGP  497 (894)
T ss_pred             cCCc
Confidence            6543

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.56  E-value=1.8e-07  Score=92.35  Aligned_cols=78  Identities=28%  Similarity=0.385  Sum_probs=69.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHh-CCceeCCeeEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF-NGQKFGKRPIAV  290 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l-~~~~~~g~~i~v  290 (676)
                      ......+|||++|-..++|.+|+++|-+||.|.++.+..      .+++|||+|.+.++|+.|..++ +...|.|.+|.|
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~------~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILP------RKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKI  297 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeec------ccccceeeehhhHHHHHHHHhhcceeeecceEEEE
Confidence            344568999999999999999999999999999999987      4578999999999999998864 555679999999


Q ss_pred             EEecC
Q 005812          291 DWAVP  295 (676)
Q Consensus       291 ~~a~~  295 (676)
                      .|+.+
T Consensus       298 ~Wg~~  302 (377)
T KOG0153|consen  298 KWGRP  302 (377)
T ss_pred             EeCCC
Confidence            99987

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.55  E-value=1.9e-07  Score=96.97  Aligned_cols=86  Identities=23%  Similarity=0.346  Sum_probs=78.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ....+++|+|.+|...+-..||+++|++||.|+-.+|+.+..+--.++|+||++.+..+|.+||..|+     .+.|.||
T Consensus       401 rs~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLH-----rTELHGr  475 (940)
T KOG4661|consen  401 RSTLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLH-----RTELHGR  475 (940)
T ss_pred             ccccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhh-----hhhhcce
Confidence            45567899999999999999999999999999999999887666679999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|..++...
T Consensus       476 mISVEkaKNEp  486 (940)
T KOG4661|consen  476 MISVEKAKNEP  486 (940)
T ss_pred             eeeeeecccCc
Confidence            99999987643

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.54  E-value=1.3e-07  Score=98.24  Aligned_cols=83  Identities=19%  Similarity=0.324  Sum_probs=76.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ...+.|||.+|+..+-..+|+.+|++||.|+..+++.+..+.-.++|+||++.+.++|.+||..|+.+.|.|+.|.|+.+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            34689999999999999999999999999999999998877778999999999999999999999999999999999987


Q ss_pred             cCC
Q 005812          294 VPK  296 (676)
Q Consensus       294 ~~~  296 (676)
                      +..
T Consensus       483 KNE  485 (940)
T KOG4661|consen  483 KNE  485 (940)
T ss_pred             ccC
Confidence            653

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.48  E-value=8.8e-08  Score=105.17  Aligned_cols=162  Identities=21%  Similarity=0.212  Sum_probs=134.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      .+++||++||+..+++.+|+..|..+|.|.+|.|-+.+ -+.-..||||.|.+...+-.|...+.+..|....+++.+..
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            46899999999999999999999999999999887653 34455789999999999999999888888766666655543


Q ss_pred             CCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCC
Q 005812          295 PKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSL  374 (676)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  374 (676)
                      ++                                                                              
T Consensus       450 ~k------------------------------------------------------------------------------  451 (975)
T KOG0112|consen  450 PK------------------------------------------------------------------------------  451 (975)
T ss_pred             cc------------------------------------------------------------------------------
Confidence            31                                                                              


Q ss_pred             CCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE
Q 005812          375 SDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS  454 (676)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~  454 (676)
                                                                     ..+.+.+++++|+.-+....|...|..||.|..
T Consensus       452 -----------------------------------------------st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~  484 (975)
T KOG0112|consen  452 -----------------------------------------------STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRI  484 (975)
T ss_pred             -----------------------------------------------cccceeeccCCCCCCChHHHHHHHhhccCccee
Confidence                                                           112468999999999999999999999999998


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC--cEEEEEEccCchhh
Q 005812          455 FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG--RQLTVLKALDKKLA  513 (676)
Q Consensus       455 v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g--r~l~v~~a~~k~~~  513 (676)
                      |.+-      ...-||+|.|.+...|+.|+..|.     |..|+|  +.|.|.++......
T Consensus       485 Idy~------hgq~yayi~yes~~~aq~a~~~~r-----gap~G~P~~r~rvdla~~~~~~  534 (975)
T KOG0112|consen  485 IDYR------HGQPYAYIQYESPPAAQAATHDMR-----GAPLGGPPRRLRVDLASPPGAT  534 (975)
T ss_pred             eecc------cCCcceeeecccCccchhhHHHHh-----cCcCCCCCcccccccccCCCCC
Confidence            6542      235699999999999999999999     888875  68999998875533

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.42  E-value=7.2e-07  Score=86.53  Aligned_cols=83  Identities=23%  Similarity=0.390  Sum_probs=75.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      ..|+|.|||+.|+++||+++|..||.+..+-+-++ .+|.+.|.|-|.|...++|.+|++.++     ++.++|++|.+.
T Consensus        84 ~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~-~~G~s~Gta~v~~~r~~DA~~avk~~~-----gv~ldG~~mk~~  157 (243)
T KOG0533|consen   84 TKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD-RAGRSLGTADVSFNRRDDAERAVKKYN-----GVALDGRPMKIE  157 (243)
T ss_pred             ceeeeecCCcCcchHHHHHHHHHhccceEEeeccC-CCCCCCccceeeecchHhHHHHHHHhc-----CcccCCceeeeE
Confidence            68999999999999999999999998888866666 579999999999999999999999999     999999999999


Q ss_pred             EccCchhhh
Q 005812          506 KALDKKLAH  514 (676)
Q Consensus       506 ~a~~k~~~~  514 (676)
                      ...+.....
T Consensus       158 ~i~~~~~~~  166 (243)
T KOG0533|consen  158 IISSPSQSK  166 (243)
T ss_pred             EecCccccc
Confidence            887765443

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.36  E-value=1.3e-06  Score=84.84  Aligned_cols=85  Identities=27%  Similarity=0.458  Sum_probs=76.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ......|+|.|||+.++++||+++|..||.+..+.+-.++ .|.+.|.|-|.|...++|.+|++.++|..+.|+.|.+..
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3445789999999999999999999999999999888875 788999999999999999999999999999999999998


Q ss_pred             ecCCCC
Q 005812          293 AVPKNI  298 (676)
Q Consensus       293 a~~~~~  298 (676)
                      ..+...
T Consensus       159 i~~~~~  164 (243)
T KOG0533|consen  159 ISSPSQ  164 (243)
T ss_pred             ecCccc
Confidence            766544

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.35  E-value=3.5e-06  Score=69.80  Aligned_cols=79  Identities=22%  Similarity=0.173  Sum_probs=69.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHh--CCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec----C
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSA--FGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK----G  499 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~--~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~----g  499 (676)
                      +||.|+|||-..|.++|.+++..  .|....++++.|..++...|||||.|.+++.|.+..+.++     |..+.    .
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~-----g~~w~~~~s~   76 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFN-----GKKWPNFNSK   76 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHc-----CCccccCCCC
Confidence            58999999999999999998876  3778889999999889999999999999999999999999     88775    5


Q ss_pred             cEEEEEEccC
Q 005812          500 RQLTVLKALD  509 (676)
Q Consensus       500 r~l~v~~a~~  509 (676)
                      +...|.||.-
T Consensus        77 Kvc~i~yAri   86 (97)
T PF04059_consen   77 KVCEISYARI   86 (97)
T ss_pred             cEEEEehhHh
Confidence            6777888753

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.22  E-value=2.6e-06  Score=89.46  Aligned_cols=79  Identities=27%  Similarity=0.356  Sum_probs=68.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      ..+|||+|||++++..+|.++|..||.|+...|......+...+||||+|.+..+++.|+.+-      -..++|++|.|
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As------p~~ig~~kl~V  361 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS------PLEIGGRKLNV  361 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC------ccccCCeeEEE
Confidence            456999999999999999999999999999988776533444599999999999999999774      58999999999


Q ss_pred             EEccC
Q 005812          505 LKALD  509 (676)
Q Consensus       505 ~~a~~  509 (676)
                      .-..+
T Consensus       362 eek~~  366 (419)
T KOG0116|consen  362 EEKRP  366 (419)
T ss_pred             Eeccc
Confidence            87554

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.21  E-value=3.4e-06  Score=90.45  Aligned_cols=83  Identities=19%  Similarity=0.325  Sum_probs=74.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecC---CCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQ---VTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK  498 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~---~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~  498 (676)
                      ++..++|||.||++.++++.|...|..||+|.+++|+.-.   ...+.+.||||.|.+..+|++|++.|+     |..+.
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lq-----g~iv~  245 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQ-----GIIVM  245 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhc-----ceeee
Confidence            4556899999999999999999999999999999998753   345568899999999999999999999     99999


Q ss_pred             CcEEEEEEccC
Q 005812          499 GRQLTVLKALD  509 (676)
Q Consensus       499 gr~l~v~~a~~  509 (676)
                      +..+.+.|++.
T Consensus       246 ~~e~K~gWgk~  256 (877)
T KOG0151|consen  246 EYEMKLGWGKA  256 (877)
T ss_pred             eeeeeeccccc
Confidence            99999999854

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.21  E-value=1.8e-06  Score=90.62  Aligned_cols=79  Identities=23%  Similarity=0.387  Sum_probs=69.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      ..+|||+|||.+++..+|.++|..||.|....|......++..+||||+|.+.++++.|+++ +-..++++++.|+--.+
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            35599999999999999999999999999988877544455569999999999999999997 78889999999986544

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.20  E-value=1.3e-06  Score=87.44  Aligned_cols=196  Identities=17%  Similarity=0.158  Sum_probs=120.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCC---CCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDT---GLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ..|.|.||.+.++.++++.+|.-.|.|..+.|.....+   ......|||.|.+...+..|.+ |.++.|-++.|.|-.+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            38999999999999999999999999999988764322   2345689999999999998887 7888888888777654


Q ss_pred             cCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCC
Q 005812          294 VPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPS  373 (676)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  373 (676)
                      .......                                                .|.-..-..+.++..+....|.|++
T Consensus        87 ~~~~~p~------------------------------------------------r~af~~l~~~navprll~pdg~Lp~  118 (479)
T KOG4676|consen   87 GDEVIPD------------------------------------------------RFAFVELADQNAVPRLLPPDGVLPG  118 (479)
T ss_pred             CCCCCcc------------------------------------------------HHHHHhcCcccccccccCCCCccCC
Confidence            2211000                                                0000000000011111122222222


Q ss_pred             CCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCc---ccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCC
Q 005812          374 LSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQ---TEGEDELQNTIFICNLPFDLDNEEVKQRFSAFG  450 (676)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G  450 (676)
                      .....                   ...++ |.  ..-.++.+.+   ...-..-.++++|.+|+..+...++.+.|..+|
T Consensus       119 ~~~lt-------------------~~nh~-p~--ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~e~~e~f~r~G  176 (479)
T KOG4676|consen  119 DRPLT-------------------KINHS-PN--AILKTPELPPQAAAKKLEEIRRTREVQSLISAAILPESGESFERKG  176 (479)
T ss_pred             CCccc-------------------cccCC-cc--ceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcchhhhhhhhhcc
Confidence            11110                   00000 00  0000011100   001112237899999999999999999999999


Q ss_pred             ceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHc
Q 005812          451 EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS  487 (676)
Q Consensus       451 ~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l  487 (676)
                      .|.+..+-    .+....+|.|.|........|+..+
T Consensus       177 ev~ya~~a----sk~~s~~c~~sf~~qts~~halr~~  209 (479)
T KOG4676|consen  177 EVSYAHTA----SKSRSSSCSHSFRKQTSSKHALRSH  209 (479)
T ss_pred             hhhhhhhh----ccCCCcchhhhHhhhhhHHHHHHhc
Confidence            99887543    3444567889999998888888665

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.16  E-value=3.4e-06  Score=82.27  Aligned_cols=83  Identities=23%  Similarity=0.371  Sum_probs=77.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .......+||+|+.+.++.+++..+|+.||.|..+.|+.+...+.++|||||+|.+.+.+..|+. |+|..|.|+.+.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            44567899999999999999999999999999999999999998999999999999999999999 99999999999999


Q ss_pred             EecC
Q 005812          292 WAVP  295 (676)
Q Consensus       292 ~a~~  295 (676)
                      +..-
T Consensus       176 ~~r~  179 (231)
T KOG4209|consen  176 LKRT  179 (231)
T ss_pred             eeee
Confidence            8643

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.10  E-value=5e-06  Score=70.73  Aligned_cols=76  Identities=28%  Similarity=0.347  Sum_probs=50.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      ++.|+|.+++..++.++|++.|+.||.|.+|.+...      ...|||.|.+++.|+.|+..+...++++..+.+..+.+
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~   74 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTL   74 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEE
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEE
Confidence            468999999999999999999999999999876432      34789999999999999999986666678888888777


Q ss_pred             EE
Q 005812          505 LK  506 (676)
Q Consensus       505 ~~  506 (676)
                      ..
T Consensus        75 ~v   76 (105)
T PF08777_consen   75 EV   76 (105)
T ss_dssp             E-
T ss_pred             EE
Confidence            65

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.07  E-value=5.4e-06  Score=80.87  Aligned_cols=81  Identities=16%  Similarity=0.281  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      ....+||+|+.+.++.+++..+|+.||.|..+.+..+...+.++|||||+|.+.+.++.|+. |+     +..|.|+.+.
T Consensus       100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~-----gs~i~~~~i~  173 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LD-----GSEIPGPAIE  173 (231)
T ss_pred             CCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cC-----Ccccccccce
Confidence            44789999999999999999999999999999999999998999999999999999999998 99     9999999999


Q ss_pred             EEEccCc
Q 005812          504 VLKALDK  510 (676)
Q Consensus       504 v~~a~~k  510 (676)
                      |.+..-+
T Consensus       174 vt~~r~~  180 (231)
T KOG4209|consen  174 VTLKRTN  180 (231)
T ss_pred             eeeeeee
Confidence            9996643

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.03  E-value=3.5e-06  Score=88.57  Aligned_cols=73  Identities=23%  Similarity=0.415  Sum_probs=66.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIA  289 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~  289 (676)
                      .....++|+|-|||..+++++|+.+|+.||.|..|+.-+.     .+|.+||+|-+..+|++|++.|++..+.|+.|.
T Consensus        71 ~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   71 KDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            4556789999999999999999999999999999766554     678999999999999999999999999999998

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.02  E-value=3.4e-06  Score=84.43  Aligned_cols=150  Identities=11%  Similarity=0.133  Sum_probs=117.3

Q ss_pred             EEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeEE
Q 005812          123 TVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTV  202 (676)
Q Consensus       123 ~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~i  202 (676)
                      .|.|.||.+.++.++++.||.-.|.|.++.|+..-..      ..-.-....|||.|.+...+..|.. |.++.+-+..+
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d------~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdral   81 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDD------SKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRAL   81 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCC------ccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeE
Confidence            6899999999999999999999999999997753221      1112346789999999999998866 88888888887


Q ss_pred             EEecCCCCC----------------------------------------------C----------CCCCcEEEEcCCCC
Q 005812          203 WARQLGGEG----------------------------------------------S----------KTQKWKLIIRNIPF  226 (676)
Q Consensus       203 ~v~~~~~~~----------------------------------------------~----------~~~~~~v~V~nLp~  226 (676)
                      .|.++....                                              .          ..-.++++|.+|+.
T Consensus        82 iv~p~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~  161 (479)
T KOG4676|consen   82 IVRPYGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLIS  161 (479)
T ss_pred             EEEecCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchh
Confidence            765332100                                              0          00137899999999


Q ss_pred             CCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC
Q 005812          227 KAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG  284 (676)
Q Consensus       227 ~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~  284 (676)
                      .+...++.++|..+|.|....+..    +....+|-|.|........|+.. +|..+.
T Consensus       162 ~~~l~e~~e~f~r~Gev~ya~~as----k~~s~~c~~sf~~qts~~halr~-~gre~k  214 (479)
T KOG4676|consen  162 AAILPESGESFERKGEVSYAHTAS----KSRSSSCSHSFRKQTSSKHALRS-HGRERK  214 (479)
T ss_pred             hhcchhhhhhhhhcchhhhhhhhc----cCCCcchhhhHhhhhhHHHHHHh-cchhhh
Confidence            999999999999999998776654    33556788999999999999994 787765

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.98  E-value=3.8e-05  Score=60.33  Aligned_cols=67  Identities=12%  Similarity=0.153  Sum_probs=47.2

Q ss_pred             EEEEcCCCccccHHH----HHHHhhcCC-CeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCee
Q 005812          123 TVIIGGLLNADMAEE----VHRLAGSIG-TVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEI  197 (676)
Q Consensus       123 ~l~V~nLp~~~~~~~----l~~~F~~~G-~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~  197 (676)
                      .|+|.|||.+.+...    |+.++..|| .|.+|.                   .+.|+|.|.+.+.|.+|.+.|+|..+
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~-------------------~~tAilrF~~~~~A~RA~KRmegEdV   64 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS-------------------GGTAILRFPNQEFAERAQKRMEGEDV   64 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE---------------------TT-EEEEESSHHHHHHHHHHHTT--S
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe-------------------CCEEEEEeCCHHHHHHHHHhhccccc
Confidence            589999999877544    667787887 787775                   35699999999999999999999999


Q ss_pred             cCeEEEEecCC
Q 005812          198 KGGTVWARQLG  208 (676)
Q Consensus       198 ~~~~i~v~~~~  208 (676)
                      .|..|.++...
T Consensus        65 fG~kI~v~~~~   75 (90)
T PF11608_consen   65 FGNKISVSFSP   75 (90)
T ss_dssp             SSS--EEESS-
T ss_pred             ccceEEEEEcC
Confidence            99999997653

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.95  E-value=7.9e-07  Score=89.53  Aligned_cols=153  Identities=21%  Similarity=0.266  Sum_probs=121.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCce-eCCeeEEEEEecC
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK-FGKRPIAVDWAVP  295 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~-~~g~~i~v~~a~~  295 (676)
                      ..+|++||.+.++..+|..+|...-.-.+-.++.      ..||+||.+.+...|.+|++.++|.. +.|.++.|.++.+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            3689999999999999999997531111111122      34899999999999999999999874 7899999998876


Q ss_pred             CCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCC
Q 005812          296 KNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLS  375 (676)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  375 (676)
                      +...                                                                            
T Consensus        76 kkqr----------------------------------------------------------------------------   79 (584)
T KOG2193|consen   76 KKQR----------------------------------------------------------------------------   79 (584)
T ss_pred             HHHH----------------------------------------------------------------------------
Confidence            5421                                                                            


Q ss_pred             CccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEE
Q 005812          376 DDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSF  455 (676)
Q Consensus       376 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v  455 (676)
                                                                       ++.+-|+|+|...-++-|..+...||.+..|
T Consensus        80 -------------------------------------------------srk~Qirnippql~wevld~Ll~qyg~ve~~  110 (584)
T KOG2193|consen   80 -------------------------------------------------SRKIQIRNIPPQLQWEVLDSLLAQYGTVENC  110 (584)
T ss_pred             -------------------------------------------------hhhhhHhcCCHHHHHHHHHHHHhccCCHhHh
Confidence                                                             2468899999999999999999999999998


Q ss_pred             EEe-ecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccC
Q 005812          456 VPV-LHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALD  509 (676)
Q Consensus       456 ~i~-~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~  509 (676)
                      ..+ .+.+    .-..=|+|.+.+.+..|+.+++     |..|....+.+.|-..
T Consensus       111 eqvnt~~e----tavvnvty~~~~~~~~ai~kl~-----g~Q~en~~~k~~YiPd  156 (584)
T KOG2193|consen  111 EQVNTDSE----TAVVNVTYSAQQQHRQAIHKLN-----GPQLENQHLKVGYIPD  156 (584)
T ss_pred             hhhccchH----HHHHHHHHHHHHHHHHHHHhhc-----chHhhhhhhhcccCch
Confidence            543 2322    2223478999999999999999     9999999999998544

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.87  E-value=4.1e-06  Score=84.50  Aligned_cols=143  Identities=19%  Similarity=0.210  Sum_probs=111.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      ..+||+||.+.++..||..+|...-.-.+-.++      ...||+||.+.+...|.+|++.+++    ...+.|.++.|.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl------~k~gyafvd~pdq~wa~kaie~~sg----k~elqGkr~e~~   71 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFL------VKSGYAFVDCPDQQWANKAIETLSG----KVELQGKRQEVE   71 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCccee------eecceeeccCCchhhhhhhHHhhch----hhhhcCceeecc
Confidence            469999999999999999999864111111112      2368999999999999999999982    478899999999


Q ss_pred             EccCchhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCeEEEecC
Q 005812          506 KALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNL  585 (676)
Q Consensus       506 ~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~V~nl  585 (676)
                      ...++....                                                               +.+.|+|+
T Consensus        72 ~sv~kkqrs---------------------------------------------------------------rk~Qirni   88 (584)
T KOG2193|consen   72 HSVPKKQRS---------------------------------------------------------------RKIQIRNI   88 (584)
T ss_pred             chhhHHHHh---------------------------------------------------------------hhhhHhcC
Confidence            987764221                                                               35889999


Q ss_pred             CcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCC
Q 005812          586 PKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPS  659 (676)
Q Consensus       586 p~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~  659 (676)
                      |...-.+-|..+..         +||.|..|....-.         .-...--|.|.+.+.+..||..|||+-+
T Consensus        89 ppql~wevld~Ll~---------qyg~ve~~eqvnt~---------~etavvnvty~~~~~~~~ai~kl~g~Q~  144 (584)
T KOG2193|consen   89 PPQLQWEVLDSLLA---------QYGTVENCEQVNTD---------SETAVVNVTYSAQQQHRQAIHKLNGPQL  144 (584)
T ss_pred             CHHHHHHHHHHHHh---------ccCCHhHhhhhccc---------hHHHHHHHHHHHHHHHHHHHHhhcchHh
Confidence            99999999999999         79999998664221         1234556789999999999999999654

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.87  E-value=2.3e-05  Score=84.35  Aligned_cols=85  Identities=20%  Similarity=0.268  Sum_probs=73.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCC---CCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTD---TGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIA  289 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~---~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~  289 (676)
                      .+..+.+||+||++.++++.|...|..||+|.+++|+..+.   ..+.+-+|||-|-+..+|++|++.|+|..+.+..++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            45578999999999999999999999999999999986432   234556799999999999999999999999999999


Q ss_pred             EEEecCCC
Q 005812          290 VDWAVPKN  297 (676)
Q Consensus       290 v~~a~~~~  297 (676)
                      +-|+++-.
T Consensus       251 ~gWgk~V~  258 (877)
T KOG0151|consen  251 LGWGKAVP  258 (877)
T ss_pred             eccccccc
Confidence            99986543

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.85  E-value=5.1e-05  Score=59.65  Aligned_cols=69  Identities=26%  Similarity=0.379  Sum_probs=47.8

Q ss_pred             CeEEEcCCCCCCCHHH----HHHHHHhCC-ceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          426 NTIFICNLPFDLDNEE----VKQRFSAFG-EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       426 ~~l~V~nLp~~~teed----l~~~F~~~G-~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ..|+|.|||.+.+...    |+.++..+| .|..|          +.+.|+|.|.+++.|.+|.+.|+     |-.+.|+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----------~~~tAilrF~~~~~A~RA~KRme-----gEdVfG~   67 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----------SGGTAILRFPNQEFAERAQKRME-----GEDVFGN   67 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHT-----T--SSSS
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----------eCCEEEEEeCCHHHHHHHHHhhc-----ccccccc
Confidence            4799999999988655    456666776 56665          24689999999999999999999     9999999


Q ss_pred             EEEEEEccC
Q 005812          501 QLTVLKALD  509 (676)
Q Consensus       501 ~l~v~~a~~  509 (676)
                      .|.|.+...
T Consensus        68 kI~v~~~~~   76 (90)
T PF11608_consen   68 KISVSFSPK   76 (90)
T ss_dssp             --EEESS--
T ss_pred             eEEEEEcCC
Confidence            999999644

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.40  E-value=0.00036  Score=59.37  Aligned_cols=70  Identities=20%  Similarity=0.295  Sum_probs=44.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCc-----eeCCeeEEEE
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQ-----KFGKRPIAVD  291 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~-----~~~g~~i~v~  291 (676)
                      +.|.|.+++..++-++|++.|+.||.|..|.+...      ...|||.|.+++.|+.|+.++.-.     .+.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            57899999999999999999999999999988763      235999999999999999976433     4566665554


Q ss_pred             E
Q 005812          292 W  292 (676)
Q Consensus       292 ~  292 (676)
                      .
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            3

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.34  E-value=0.00041  Score=68.39  Aligned_cols=81  Identities=21%  Similarity=0.416  Sum_probs=63.2

Q ss_pred             CCeEEEcCCCCCCCHHHH------HHHHHhCCceeEEEEeecCCCC-Ccce-E-EEEEeCCHHHHHHHHHHcCCCCCCCe
Q 005812          425 QNTIFICNLPFDLDNEEV------KQRFSAFGEVVSFVPVLHQVTK-RPKG-T-GFLKFKTVEAATAAVSASKTTSGLGI  495 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl------~~~F~~~G~v~~v~i~~~~~~~-~~~g-~-afV~F~t~~~A~~Al~~l~~~~~~g~  495 (676)
                      .+-+||-+||+.+-.|++      .++|.+||.|..+.|-+...+. ..-+ + .||+|.+.++|.+|++..+     |.
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vD-----gs  188 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVD-----GS  188 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhc-----cc
Confidence            357999999999887773      4799999999997554332111 1122 2 3999999999999999999     99


Q ss_pred             eecCcEEEEEEccCc
Q 005812          496 FLKGRQLTVLKALDK  510 (676)
Q Consensus       496 ~l~gr~l~v~~a~~k  510 (676)
                      .++||.|+..|.-.|
T Consensus       189 ~~DGr~lkatYGTTK  203 (480)
T COG5175         189 LLDGRVLKATYGTTK  203 (480)
T ss_pred             cccCceEeeecCchH
Confidence            999999999987653

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.29  E-value=0.00049  Score=67.82  Aligned_cols=82  Identities=21%  Similarity=0.391  Sum_probs=65.3

Q ss_pred             CCcEEEEcCCCCCCCHHHH------HHhhccCCceEEEEEcccCCC-CCceeEE--EEEecCHHHHHHHHHHhCCceeCC
Q 005812          215 QKWKLIIRNIPFKAKVNEI------KDMFSPVGLVWNVYIPHNTDT-GLSKGFA--FVKFTCKRDAESAIQKFNGQKFGK  285 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l------~~~F~~~G~i~~v~i~~~~~~-~~~~g~a--fV~f~~~~~A~~A~~~l~~~~~~g  285 (676)
                      ...-+||-+||+.+..+++      .++|.+||.|..|.|.+...+ +...+.+  ||+|.+.++|.+||...+|..++|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            4567999999998776663      569999999999988765311 2222333  999999999999999999999999


Q ss_pred             eeEEEEEecCC
Q 005812          286 RPIAVDWAVPK  296 (676)
Q Consensus       286 ~~i~v~~a~~~  296 (676)
                      +.|+..|...+
T Consensus       193 r~lkatYGTTK  203 (480)
T COG5175         193 RVLKATYGTTK  203 (480)
T ss_pred             ceEeeecCchH
Confidence            99999887554

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.20  E-value=0.00028  Score=70.85  Aligned_cols=83  Identities=22%  Similarity=0.230  Sum_probs=75.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCe
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVS--------FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGI  495 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~--------v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~  495 (676)
                      ...+|||-+||..+++.+|.++|.++|.|..        +.|-.++.++.+++-|.|.|.++..|+.|+..++     +.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~a-----gk  139 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFA-----GK  139 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhc-----cc
Confidence            3468999999999999999999999998753        5667788899999999999999999999999999     99


Q ss_pred             eecCcEEEEEEccCch
Q 005812          496 FLKGRQLTVLKALDKK  511 (676)
Q Consensus       496 ~l~gr~l~v~~a~~k~  511 (676)
                      .+.|.+|.|.+|..+.
T Consensus       140 df~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  140 DFCGNTIKVSLAERRT  155 (351)
T ss_pred             cccCCCchhhhhhhcc
Confidence            9999999999987664

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.05  E-value=0.0006  Score=68.55  Aligned_cols=85  Identities=26%  Similarity=0.360  Sum_probs=76.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceE--------EEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVW--------NVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG  284 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~--------~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~  284 (676)
                      .....+|||-+||..+++++|..+|.++|.|.        .|.|-++++++..+|-|.|.|.+...|+.|+.-+++..|+
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            45678999999999999999999999999874        3667788899999999999999999999999999999999


Q ss_pred             CeeEEEEEecCCC
Q 005812          285 KRPIAVDWAVPKN  297 (676)
Q Consensus       285 g~~i~v~~a~~~~  297 (676)
                      +..|.|.++..+.
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999998886554

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.95  E-value=0.0017  Score=62.21  Aligned_cols=81  Identities=22%  Similarity=0.350  Sum_probs=66.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      ..|+|.||+.-++-+.+.+-|+.||.|....+..| ..+++.+-++|.|...-.|.+|+..++ ..+.+....+++..|.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~-~~g~~~~~~~~p~~Ve  109 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCR-EGGFGGTTGGRPVGVE  109 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhc-cCccccCCCCCccCCC
Confidence            37999999999999999999999999999767666 458889999999999999999999885 1222455567777776


Q ss_pred             Ecc
Q 005812          506 KAL  508 (676)
Q Consensus       506 ~a~  508 (676)
                      +..
T Consensus       110 P~e  112 (275)
T KOG0115|consen  110 PME  112 (275)
T ss_pred             hhh
Confidence            643

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.94  E-value=0.0028  Score=67.07  Aligned_cols=79  Identities=24%  Similarity=0.502  Sum_probs=65.3

Q ss_pred             CCcEEEEcCCCCCCC------HHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC-Cee
Q 005812          215 QKWKLIIRNIPFKAK------VNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG-KRP  287 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~------e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~-g~~  287 (676)
                      -...|+|-|+|.--.      ..-|..+|+++|.|....++.+..+| .+||.|++|.+..+|+.|++.|||..|. .++
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            446899999986432      23456789999999999999887666 9999999999999999999999999984 778


Q ss_pred             EEEEEec
Q 005812          288 IAVDWAV  294 (676)
Q Consensus       288 i~v~~a~  294 (676)
                      +.|..-+
T Consensus       136 f~v~~f~  142 (698)
T KOG2314|consen  136 FFVRLFK  142 (698)
T ss_pred             EEeehhh
Confidence            8886543

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.89  E-value=0.0019  Score=47.35  Aligned_cols=52  Identities=23%  Similarity=0.561  Sum_probs=42.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHH
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI  275 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~  275 (676)
                      +.|-|.|.+.+.. +.+..+|..||.|..+.+..      ..-+.||.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            4688999997776 45666899999999998873      3357999999999999985

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=96.84  E-value=0.0032  Score=52.67  Aligned_cols=78  Identities=17%  Similarity=0.226  Sum_probs=52.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEc-ccC------CCCCceeEEEEEecCHHHHHHHHHHhCCceeCCee
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIP-HNT------DTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRP  287 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~-~~~------~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  287 (676)
                      ..+.|.|-+.|+. ....|.++|++||.|.+..-. ++.      .......+-.|+|.++.+|.+||.+ ||..|.|..
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcE
Confidence            4567899999988 457888999999999876411 110      0011345889999999999999996 999998865


Q ss_pred             E-EEEEec
Q 005812          288 I-AVDWAV  294 (676)
Q Consensus       288 i-~v~~a~  294 (676)
                      | -|.+.+
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence            4 466653

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.81  E-value=0.0029  Score=46.42  Aligned_cols=52  Identities=17%  Similarity=0.185  Sum_probs=42.3

Q ss_pred             cEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHH
Q 005812          122 RTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASV  189 (676)
Q Consensus       122 ~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~  189 (676)
                      +.|-|.|.+.+..+. +...|..||+|..+.++               ......||.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~---------------~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVP---------------ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcC---------------CCCcEEEEEECCHHHHHhhC
Confidence            468899999776654 66699999999999865               22456999999999999985

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.77  E-value=0.00086  Score=64.12  Aligned_cols=74  Identities=23%  Similarity=0.325  Sum_probs=62.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCC--------CCcee----EEEEEecCHHHHHHHHHHhCCce
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDT--------GLSKG----FAFVKFTCKRDAESAIQKFNGQK  282 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~--------~~~~g----~afV~f~~~~~A~~A~~~l~~~~  282 (676)
                      ....||+++||+.+...-|+++|+.||.|-+|.+.....+        |.+.+    -|+|+|.+...|.++...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            4568999999999999999999999999999998765433        22222    37899999999999999999999


Q ss_pred             eCCeeE
Q 005812          283 FGKRPI  288 (676)
Q Consensus       283 ~~g~~i  288 (676)
                      |+|+.=
T Consensus       153 Iggkk~  158 (278)
T KOG3152|consen  153 IGGKKK  158 (278)
T ss_pred             cCCCCC
Confidence            988753

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.68  E-value=0.0063  Score=64.47  Aligned_cols=76  Identities=18%  Similarity=0.258  Sum_probs=62.8

Q ss_pred             CCeEEEcCCCCCCC------HHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec
Q 005812          425 QNTIFICNLPFDLD------NEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK  498 (676)
Q Consensus       425 ~~~l~V~nLp~~~t------eedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~  498 (676)
                      ...|+|-|+|---.      ..-|..+|+++|.+..+.++.+...| ++||.|++|.+..+|..|++.||     |..|+
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~-----G~~ld  131 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLN-----GKRLD  131 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcc-----cceec
Confidence            46899999985321      33456899999999999888886655 89999999999999999999999     88886


Q ss_pred             -CcEEEEEE
Q 005812          499 -GRQLTVLK  506 (676)
Q Consensus       499 -gr~l~v~~  506 (676)
                       .+++.|..
T Consensus       132 knHtf~v~~  140 (698)
T KOG2314|consen  132 KNHTFFVRL  140 (698)
T ss_pred             ccceEEeeh
Confidence             66777754

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.57  E-value=0.0032  Score=67.08  Aligned_cols=88  Identities=17%  Similarity=0.157  Sum_probs=72.4

Q ss_pred             hcCCCCCccccCCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChH
Q 005812          566 TKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQ  645 (676)
Q Consensus       566 ~~~~~p~~~~~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~  645 (676)
                      ...+.|..+..++.|||.||---+|.-.|+.++..        ..|.|... +| |          .-+.-|||.|.+.+
T Consensus       433 ~RvpSPsR~~~SnvlhI~nLvRPFTlgQLkelL~r--------tgg~Vee~-Wm-D----------kIKShCyV~yss~e  492 (718)
T KOG2416|consen  433 ERVPSPSRKEPSNVLHIDNLVRPFTLGQLKELLGR--------TGGNVEEF-WM-D----------KIKSHCYVSYSSVE  492 (718)
T ss_pred             ccCCCCCCCCccceEeeecccccchHHHHHHHHhh--------ccCchHHH-HH-H----------HhhcceeEecccHH
Confidence            34556666777889999999888899999999996        57777766 54 2          34678999999999


Q ss_pred             HHHHHHHHHcCCCCCCCcccCccccccc
Q 005812          646 HALVALRVLNNNPSKLFYHHCFDAADAQ  673 (676)
Q Consensus       646 ~A~~Ai~~lng~~~~~~~~~~~~~~~~~  673 (676)
                      +|...+.+|||-.|--+--+||+|.|+-
T Consensus       493 EA~atr~AlhnV~WP~sNPK~L~adf~~  520 (718)
T KOG2416|consen  493 EAAATREALHNVQWPPSNPKHLIADFVR  520 (718)
T ss_pred             HHHHHHHHHhccccCCCCCceeEeeecc
Confidence            9999999999988876777899998863

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.51  E-value=0.0049  Score=59.16  Aligned_cols=101  Identities=21%  Similarity=0.200  Sum_probs=80.9

Q ss_pred             HHHHHHHHhCCCeecCeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEE
Q 005812          184 SACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFV  263 (676)
Q Consensus       184 ~A~~A~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV  263 (676)
                      -|..|-..|++....++.+.|+...       ...|+|.||+..+..+.+.+.|+.||.|....+..| ..++..+-++|
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~-------~a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v   77 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAM-------HAELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIV   77 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeec-------cceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchh
Confidence            3566667799999999999997432       268999999999999999999999999998777666 36778888999


Q ss_pred             EecCHHHHHHHHHHhCCce----eCCeeEEEEE
Q 005812          264 KFTCKRDAESAIQKFNGQK----FGKRPIAVDW  292 (676)
Q Consensus       264 ~f~~~~~A~~A~~~l~~~~----~~g~~i~v~~  292 (676)
                      .|...-.|..|+..++-.-    ..+++.-|..
T Consensus        78 ~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   78 EFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             hhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            9999999999999764322    3455555553

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.44  E-value=0.015  Score=46.10  Aligned_cols=59  Identities=22%  Similarity=0.401  Sum_probs=44.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCC
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG  280 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~  280 (676)
                      +.+....+|+ +|..+...||.++|+.||.|. |..+.+.       -|||...+.+.|..|+..+..
T Consensus         6 P~RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    6 PSRDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             -SGCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             CCcceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            4455667777 999999999999999999987 6666542       399999999999999998753

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=96.35  E-value=0.018  Score=48.28  Aligned_cols=76  Identities=14%  Similarity=0.257  Sum_probs=51.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEE-EeecC------CCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFV-PVLHQ------VTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL  497 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~-i~~~~------~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l  497 (676)
                      ...|.|-+.|.. ....|.++|++||.|.+.. +..+.      .......+..|+|.++.+|.+||.. |     |..|
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-N-----G~i~   78 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-N-----GTIF   78 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-T-----TEEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-C-----CeEE
Confidence            367999999987 6678999999999998763 00000      0012356889999999999999964 7     9999


Q ss_pred             cCcEEE-EEEc
Q 005812          498 KGRQLT-VLKA  507 (676)
Q Consensus       498 ~gr~l~-v~~a  507 (676)
                      .|..|. |.+.
T Consensus        79 ~g~~mvGV~~~   89 (100)
T PF05172_consen   79 SGSLMVGVKPC   89 (100)
T ss_dssp             TTCEEEEEEE-
T ss_pred             cCcEEEEEEEc
Confidence            997665 6665

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.33  E-value=0.0047  Score=63.39  Aligned_cols=67  Identities=24%  Similarity=0.270  Sum_probs=57.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeec---CCC--CC--------cceEEEEEeCCHHHHHHHHHHcC
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLH---QVT--KR--------PKGTGFLKFKTVEAATAAVSASK  488 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~---~~~--~~--------~~g~afV~F~t~~~A~~Al~~l~  488 (676)
                      .-++++|.+.|||.+-.-+.|.++|+.+|.|..|+|..-   ..+  +.        .+-+|+|+|.+.+.|.+|.+.|+
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            346899999999999999999999999999999998765   222  22        25689999999999999999987

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=96.25  E-value=0.0037  Score=62.15  Aligned_cols=78  Identities=14%  Similarity=0.235  Sum_probs=68.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCc--eEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGL--VWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~--i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ..-++||+||-|.+|++||.+.....|.  +.++++..++.+|.++|||+|-..+....++-++.|-...|.|+.-.|.-
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeec
Confidence            3458999999999999999998887664  67788888989999999999999999999999999988999988777653

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.12  E-value=0.0051  Score=58.97  Aligned_cols=82  Identities=15%  Similarity=0.142  Sum_probs=64.7

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCcc----ceEEEEeCCHHHHHHHHHHhCC
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKM----DASAVLYTTVKSACASVALLHQ  194 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~----g~afV~F~~~~~A~~A~~~l~~  194 (676)
                      +....||+++||+.+...-|+++|+.||.|-.|.+-....+...+.. +.|.+.    .-|+|+|.+...|......||+
T Consensus        72 rk~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~-~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn  150 (278)
T KOG3152|consen   72 RKTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARK-RKGGNYKKLYSEGWVEFISKRVAKRIAELLNN  150 (278)
T ss_pred             ccceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHh-hcCCCccccchhHHHHHHHHHHHHHHHHHhCC
Confidence            35568999999999999999999999999999998766654332211 112222    2379999999999999999999


Q ss_pred             CeecCeE
Q 005812          195 KEIKGGT  201 (676)
Q Consensus       195 ~~~~~~~  201 (676)
                      ..|+|+.
T Consensus       151 ~~Iggkk  157 (278)
T KOG3152|consen  151 TPIGGKK  157 (278)
T ss_pred             CccCCCC
Confidence            9999873

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.00  E-value=0.019  Score=55.97  Aligned_cols=78  Identities=21%  Similarity=0.308  Sum_probs=60.7

Q ss_pred             CeEEEcCC--CCCCC---HHHHHHHHHhCCceeEEEEeecCCCCCc-ceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          426 NTIFICNL--PFDLD---NEEVKQRFSAFGEVVSFVPVLHQVTKRP-KGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       426 ~~l~V~nL--p~~~t---eedl~~~F~~~G~v~~v~i~~~~~~~~~-~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      +.|.++|+  +-.++   ++++++-+.+||.|..|.|+..+.--.. ---.||+|...++|.+|+-.||     |.+|+|
T Consensus       282 kvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~Vdln-----GRyFGG  356 (378)
T KOG1996|consen  282 KVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLN-----GRYFGG  356 (378)
T ss_pred             HHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcC-----Cceecc
Confidence            45777776  33444   5688999999999999977766421111 2346999999999999999999     999999


Q ss_pred             cEEEEEEcc
Q 005812          500 RQLTVLKAL  508 (676)
Q Consensus       500 r~l~v~~a~  508 (676)
                      |.+...|..
T Consensus       357 r~v~A~Fyn  365 (378)
T KOG1996|consen  357 RVVSACFYN  365 (378)
T ss_pred             eeeeheecc
Confidence            999988853

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.82  E-value=0.02  Score=55.85  Aligned_cols=66  Identities=26%  Similarity=0.240  Sum_probs=54.1

Q ss_pred             HHHHHHhhccCCceEEEEEcccCCCCCc-eeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          230 VNEIKDMFSPVGLVWNVYIPHNTDTGLS-KGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       230 e~~l~~~F~~~G~i~~v~i~~~~~~~~~-~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      ++++.+.+.+||.|..|.|...+..... .--.||+|...++|.+|+-.|||..|+|+.+..+|..-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccH
Confidence            4678889999999999988766532211 22379999999999999999999999999999988753

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=95.70  E-value=0.011  Score=63.08  Aligned_cols=80  Identities=14%  Similarity=0.278  Sum_probs=65.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhcc-CCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee---CCee
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSP-VGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF---GKRP  287 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~-~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~---~g~~  287 (676)
                      .....+.|+|.||-.-+|.-+|+.++.+ .|.|+..+|-+      -+..|||.|.+.++|.....+|||..+   .++.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDk------IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDK------IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHH------hhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            3445789999999999999999999985 56666664433      456799999999999999999999988   5678


Q ss_pred             EEEEEecCCC
Q 005812          288 IAVDWAVPKN  297 (676)
Q Consensus       288 i~v~~a~~~~  297 (676)
                      |.+.|.....
T Consensus       514 L~adf~~~de  523 (718)
T KOG2416|consen  514 LIADFVRADE  523 (718)
T ss_pred             eEeeecchhH
Confidence            8888875543

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.66  E-value=0.0049  Score=59.31  Aligned_cols=63  Identities=22%  Similarity=0.374  Sum_probs=52.4

Q ss_pred             HHHHHhhc-cCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          231 NEIKDMFS-PVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       231 ~~l~~~F~-~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ++|...|+ +||.|+.+.|-.+. .-.-.|-+||.|..+++|++|+..||+..|.|++|..+++.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            56666666 89999998776543 23356779999999999999999999999999999999873

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.47  E-value=0.0072  Score=58.21  Aligned_cols=63  Identities=21%  Similarity=0.313  Sum_probs=52.3

Q ss_pred             HHHHHHHH-hCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEcc
Q 005812          440 EEVKQRFS-AFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKAL  508 (676)
Q Consensus       440 edl~~~F~-~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~  508 (676)
                      |||...|+ +||.|+.+.|-.+. .-...|-+||.|...++|++|+..||     +..+.|++|+..+..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~ln-----nRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLN-----NRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHc-----CccccCCcceeeecC
Confidence            56666666 89999998655443 23457899999999999999999999     999999999999854

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=95.46  E-value=0.02  Score=58.95  Aligned_cols=71  Identities=25%  Similarity=0.301  Sum_probs=55.8

Q ss_pred             ccCCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCc--------ceEEEEEeCChHH
Q 005812          575 VSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYS--------RGVAFVEFTEHQH  646 (676)
Q Consensus       575 ~~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s--------~g~afV~F~~~~~  646 (676)
                      .+..+|.+-|||.+-.-+.|.++|+         .+|.|+.|+|+.--... .+..+.+        +-+|+|+|+..+.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg---------~~G~IksIRIckPgaip-~d~r~~~~~~~~~~tk~~AlvEye~~~~  298 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFG---------TVGSIKSIRICKPGAIP-EDVRGFPKKYFELQTKECALVEYEEVEA  298 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhh---------cccceeeeeecCCCCCC-cccccCCccchhhhhhhhhhhhhhhhHH
Confidence            3557899999999999999999999         59999999998661110 1111222        4589999999999


Q ss_pred             HHHHHHHHc
Q 005812          647 ALVALRVLN  655 (676)
Q Consensus       647 A~~Ai~~ln  655 (676)
                      |.+|.+.||
T Consensus       299 A~KA~e~~~  307 (484)
T KOG1855|consen  299 ARKARELLN  307 (484)
T ss_pred             HHHHHHhhc
Confidence            999999984

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.36  E-value=0.086  Score=46.98  Aligned_cols=76  Identities=16%  Similarity=0.197  Sum_probs=52.9

Q ss_pred             CCCCcEEEEcCCC------CCCCH---HHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 005812          213 KTQKWKLIIRNIP------FKAKV---NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF  283 (676)
Q Consensus       213 ~~~~~~v~V~nLp------~~~~e---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  283 (676)
                      .++..+|.|.=+.      ...++   .+|.+.|..||.+.-+++.-+        --+|+|.+...|-+|+. ++|..+
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v   94 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQV   94 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEE
Confidence            3455677777555      12332   367888999999888887754        27999999999999999 699999


Q ss_pred             CCeeEEEEEecCCC
Q 005812          284 GKRPIAVDWAVPKN  297 (676)
Q Consensus       284 ~g~~i~v~~a~~~~  297 (676)
                      +|+.|.|....|..
T Consensus        95 ~g~~l~i~LKtpdW  108 (146)
T PF08952_consen   95 NGRTLKIRLKTPDW  108 (146)
T ss_dssp             TTEEEEEEE-----
T ss_pred             CCEEEEEEeCCccH
Confidence            99999999876643

; PDB: 1UFW_A 2DNR_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.33  E-value=0.096  Score=39.43  Aligned_cols=57  Identities=16%  Similarity=0.203  Sum_probs=45.4

Q ss_pred             CeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHH
Q 005812          578 TRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVL  654 (676)
Q Consensus       578 ~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~l  654 (676)
                      ..|+|+++. .++.++|+.+|.+|+      ......+|.++-|             ..|-|-|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~------~~~~~~~IEWIdD-------------tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYF------DEEGPFRIEWIDD-------------TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhc------ccCCCceEEEecC-------------CcEEEEECCHHHHHHHHHcC
Confidence            579999996 689999999999752      1123456888755             37899999999999999875

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=95.20  E-value=0.029  Score=56.01  Aligned_cols=77  Identities=14%  Similarity=0.211  Sum_probs=66.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCC--ceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFG--EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G--~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      .++||+||-|-+|++||.+.....|  .+..++++.+..+|.++|||+|-..+.....+.++-|-     ...|.|..-.
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP-----~k~iHGQ~P~  155 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILP-----TKTIHGQSPT  155 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcc-----cceecCCCCe
Confidence            5899999999999999999998877  46667888888899999999999999988889998888     8899888555


Q ss_pred             EEEc
Q 005812          504 VLKA  507 (676)
Q Consensus       504 v~~a  507 (676)
                      |...
T Consensus       156 V~~~  159 (498)
T KOG4849|consen  156 VLSY  159 (498)
T ss_pred             eecc
Confidence            5443

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=94.70  E-value=0.11  Score=41.25  Aligned_cols=57  Identities=19%  Similarity=0.328  Sum_probs=44.3

Q ss_pred             CCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcC
Q 005812          577 RTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN  656 (676)
Q Consensus       577 ~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng  656 (676)
                      +.-||--..|..+-..||.++|+         +||.|. |.++-|             ..|||.....+.|..|+..++-
T Consensus         8 RdHVFhltFPkeWK~~DI~qlFs---------pfG~I~-VsWi~d-------------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    8 RDHVFHLTFPKEWKTSDIYQLFS---------PFGQIY-VSWIND-------------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             GCCEEEEE--TT--HHHHHHHCC---------CCCCEE-EEEECT-------------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             cceEEEEeCchHhhhhhHHHHhc---------cCCcEE-EEEEcC-------------CcEEEEeecHHHHHHHHHHhcc
Confidence            33455545999999999999999         799986 888754             5899999999999999999975

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=94.63  E-value=0.16  Score=45.32  Aligned_cols=56  Identities=32%  Similarity=0.455  Sum_probs=44.2

Q ss_pred             HHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccC
Q 005812          440 EEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALD  509 (676)
Q Consensus       440 edl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~  509 (676)
                      .+|.+.|..||.+.-++++-+        .-+|+|.+-+.|.+|+ .++     |..++|+.|.|....+
T Consensus        51 ~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaal-s~d-----g~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAAL-SLD-----GIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHH-HGC-----CSEETTEEEEEEE---
T ss_pred             HHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHH-ccC-----CcEECCEEEEEEeCCc
Confidence            377888999999888776532        3689999999999998 578     9999999999998543

; PDB: 1UFW_A 2DNR_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.48  E-value=0.22  Score=37.56  Aligned_cols=53  Identities=23%  Similarity=0.333  Sum_probs=42.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhC----CceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHc
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAF----GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS  487 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~----G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l  487 (676)
                      ..|+|+|+. +.+.+||+.+|..|    + ...|..+-|.       .|=|.|.+.+.|.+||.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~-~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEG-PFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCC-CceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            489999996 68899999999999    4 3455555442       3679999999999999865

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=94.27  E-value=0.71  Score=45.73  Aligned_cols=207  Identities=16%  Similarity=0.202  Sum_probs=124.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecC-------CCCCcceEEEEEeCCHHHHHH----HHHHcCCCC
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQ-------VTKRPKGTGFLKFKTVEAATA----AVSASKTTS  491 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~-------~~~~~~g~afV~F~t~~~A~~----Al~~l~~~~  491 (676)
                      -.++.|.+.|+..+++--.+...|-+||+|++|+++.+.       ..........+.|-+.+.+..    .++.|+++ 
T Consensus        13 YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEf-   91 (309)
T PF10567_consen   13 YRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEF-   91 (309)
T ss_pred             ceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHH-
Confidence            346889999999999999999999999999999998765       122345678899999887653    34555533 


Q ss_pred             CCCeeecCcEEEEEEccCchhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCC-C
Q 005812          492 GLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQ-S  570 (676)
Q Consensus       492 ~~g~~l~gr~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~  570 (676)
                        ...+....|.|.+..-+-......       +....+                  +  .++.         ...+. +
T Consensus        92 --K~~L~S~~L~lsFV~l~y~~~~~~-------~~~~~~------------------~--~~~~---------~~~L~~~  133 (309)
T PF10567_consen   92 --KTKLKSESLTLSFVSLNYQKKTDP-------NDEEAD------------------F--SDYL---------VASLQYN  133 (309)
T ss_pred             --HHhcCCcceeEEEEEEeccccccc-------cccccc------------------h--hhHH---------hhhhhhe
Confidence              467778888888865321100000       000000                  0  0000         00011 0


Q ss_pred             CCccccCCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHH
Q 005812          571 PNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVA  650 (676)
Q Consensus       571 p~~~~~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~A  650 (676)
                      --...+.+.|.|- +...+..+++..---.+.....-+-| .|++|.|+--...    ...=+.-||.+.|-+..-|...
T Consensus       134 i~~~gATRSl~Ie-F~~~~~~~dl~~~kL~fL~~~~n~RY-VlEsIDlVna~~~----~~~Fp~~YaILtFlnIsMAiEV  207 (309)
T PF10567_consen  134 IINRGATRSLAIE-FKDPVDKDDLIEKKLPFLKNSNNKRY-VLESIDLVNADEP----SKHFPKNYAILTFLNISMAIEV  207 (309)
T ss_pred             eecCCcceEEEEE-ecCccchhHHHHHhhhhhccCCCceE-EEEEEEEeccCcc----cccCCcceEEEeehhHHhHHHH
Confidence            0011133557665 44555443332222222221111112 5777888743221    2334567999999999999999


Q ss_pred             HHHHcCCCCCCCcccCcccccccc
Q 005812          651 LRVLNNNPSKLFYHHCFDAADAQC  674 (676)
Q Consensus       651 i~~lng~~~~~~~~~~~~~~~~~~  674 (676)
                      +.-|..+..-.|=.+|..|+-+.+
T Consensus       208 ~dYlk~~~~~~~Iskc~fVs~~~~  231 (309)
T PF10567_consen  208 LDYLKSNSKKLGISKCFFVSVQPH  231 (309)
T ss_pred             HHHHHhcccccCcceEEEEeccCc
Confidence            999987766678889999887664

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=94.27  E-value=0.092  Score=49.34  Aligned_cols=82  Identities=20%  Similarity=0.262  Sum_probs=52.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhcc-CCce---EEEE--EcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC---
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSP-VGLV---WNVY--IPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG---  284 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~-~G~i---~~v~--i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~---  284 (676)
                      .....|.|++||+++|++++++.++. ++.-   ..+.  ..........-.-|||.|.+.+++......++|..|.   
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34568999999999999999998887 6665   2333  2221111223446999999999999999999998872   


Q ss_pred             C--eeEEEEEecC
Q 005812          285 K--RPIAVDWAVP  295 (676)
Q Consensus       285 g--~~i~v~~a~~  295 (676)
                      |  ....|++|.-
T Consensus        85 g~~~~~~VE~Apy   97 (176)
T PF03467_consen   85 GNEYPAVVEFAPY   97 (176)
T ss_dssp             S-EEEEEEEE-SS
T ss_pred             CCCcceeEEEcch
Confidence            2  3556777744

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.44  E-value=0.34  Score=42.59  Aligned_cols=71  Identities=27%  Similarity=0.283  Sum_probs=53.6

Q ss_pred             CCCeEEEcCCCCCC----CHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          424 LQNTIFICNLPFDL----DNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       424 ~~~~l~V~nLp~~~----teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      +-.+|.|+=|...+    +-..|....+.||+|.+|...     |  +..|.|.|.+..+|-+|+.++.      ...-|
T Consensus        85 PMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~------s~~pg  151 (166)
T PF15023_consen   85 PMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQ------SRAPG  151 (166)
T ss_pred             CceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhc------CCCCC
Confidence            44688887665554    334455667789999998643     3  5679999999999999999997      46678


Q ss_pred             cEEEEEEc
Q 005812          500 RQLTVLKA  507 (676)
Q Consensus       500 r~l~v~~a  507 (676)
                      ..+.+.|-
T Consensus       152 tm~qCsWq  159 (166)
T PF15023_consen  152 TMFQCSWQ  159 (166)
T ss_pred             ceEEeecc
Confidence            88888884

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=93.18  E-value=0.036  Score=55.78  Aligned_cols=83  Identities=20%  Similarity=0.380  Sum_probs=64.7

Q ss_pred             CeEEEcCCCCCCCHHHHH---HHHHhCCceeEEEEeecCC--CC-CcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          426 NTIFICNLPFDLDNEEVK---QRFSAFGEVVSFVPVLHQV--TK-RPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~---~~F~~~G~v~~v~i~~~~~--~~-~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      +-+||-+|+..+..+.+.   ++|.+||.|..|.+..+..  .+ ....-++|+|...++|..||...+     |+.++|
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~-----g~~~dg  152 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVD-----GFVDDG  152 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhh-----hHHhhh
Confidence            568888899887666664   4899999999987766541  11 112338999999999999999999     999999


Q ss_pred             cEEEEEEccCchhh
Q 005812          500 RQLTVLKALDKKLA  513 (676)
Q Consensus       500 r~l~v~~a~~k~~~  513 (676)
                      +.|...+...+-..
T Consensus       153 ~~lka~~gttkycs  166 (327)
T KOG2068|consen  153 RALKASLGTTKYCS  166 (327)
T ss_pred             hhhHHhhCCCcchh
Confidence            99988887766543

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=92.64  E-value=0.16  Score=47.73  Aligned_cols=81  Identities=17%  Similarity=0.157  Sum_probs=51.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHh-CCce---eEEEEeecC--CCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSA-FGEV---VSFVPVLHQ--VTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK  498 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~-~G~v---~~v~i~~~~--~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~  498 (676)
                      ...|.|++||+..|++++.+.++. ++.-   .++.-....  .......-|||.|.+.+++......++     |..|-
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~-----g~~F~   81 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFD-----GHVFV   81 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCT-----TEEEE
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcC-----CcEEE
Confidence            468999999999999999997777 6655   333211221  111234569999999999999999999     76664


Q ss_pred             C-----cEEEEEEccCc
Q 005812          499 G-----RQLTVLKALDK  510 (676)
Q Consensus       499 g-----r~l~v~~a~~k  510 (676)
                      +     .+-.|.+|.-.
T Consensus        82 D~kg~~~~~~VE~Apyq   98 (176)
T PF03467_consen   82 DSKGNEYPAVVEFAPYQ   98 (176)
T ss_dssp             -TTS-EEEEEEEE-SS-
T ss_pred             CCCCCCcceeEEEcchh
Confidence            2     25567776653

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=92.30  E-value=0.39  Score=51.36  Aligned_cols=94  Identities=18%  Similarity=0.300  Sum_probs=68.3

Q ss_pred             HHHHHHHHHhCCCeecCeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhcc--CCceEEEEEcccCCCCCceeE
Q 005812          183 KSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSP--VGLVWNVYIPHNTDTGLSKGF  260 (676)
Q Consensus       183 ~~A~~A~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~--~G~i~~v~i~~~~~~~~~~g~  260 (676)
                      +--..++...-+..+..+-..|+      .....|.|+++-||..+..++|+.+|+.  +-.+.+|.+-.+.      + 
T Consensus       148 dLI~Evlresp~VqvDekgekVr------p~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------n-  214 (684)
T KOG2591|consen  148 DLIVEVLRESPNVQVDEKGEKVR------PNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------N-  214 (684)
T ss_pred             HHHHHHHhcCCCceeccCccccc------cCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------c-
Confidence            33345556566666666666665      3456788999999999999999999985  5667888876642      2 


Q ss_pred             EEEEecCHHHHHHHHHHhCC--ceeCCeeEE
Q 005812          261 AFVKFTCKRDAESAIQKFNG--QKFGKRPIA  289 (676)
Q Consensus       261 afV~f~~~~~A~~A~~~l~~--~~~~g~~i~  289 (676)
                      =||+|.+..||+.|.+.|.-  ..|.|+.|-
T Consensus       215 WyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  215 WYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             eEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            48999999999999886642  235555543

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=91.98  E-value=0.081  Score=53.34  Aligned_cols=82  Identities=15%  Similarity=0.275  Sum_probs=63.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHH---HhhccCCceEEEEEcccCC----CCCceeEEEEEecCHHHHHHHHHHhCCceeCCe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIK---DMFSPVGLVWNVYIPHNTD----TGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKR  286 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~---~~F~~~G~i~~v~i~~~~~----~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  286 (676)
                      ....-+||-+|+.....+.+.   +.|.+||.|..|.+.+++.    .+.. .-+||+|...++|..||...+|..+.|+
T Consensus        75 Vqknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~-~s~yITy~~~eda~rci~~v~g~~~dg~  153 (327)
T KOG2068|consen   75 VQKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGT-CSVYITYEEEEDADRCIDDVDGFVDDGR  153 (327)
T ss_pred             hhhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCC-CcccccccchHhhhhHHHHhhhHHhhhh
Confidence            344678888998886655553   4889999999999888652    1211 2289999999999999999999999999


Q ss_pred             eEEEEEecCC
Q 005812          287 PIAVDWAVPK  296 (676)
Q Consensus       287 ~i~v~~a~~~  296 (676)
                      .++..+...+
T Consensus       154 ~lka~~gttk  163 (327)
T KOG2068|consen  154 ALKASLGTTK  163 (327)
T ss_pred             hhHHhhCCCc
Confidence            9888776554

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=91.71  E-value=0.53  Score=46.62  Aligned_cols=73  Identities=19%  Similarity=0.286  Sum_probs=56.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCee-EEEEEec
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRP-IAVDWAV  294 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~-i~v~~a~  294 (676)
                      ..-|-|-++|+.-. ..|..+|++||.|.......      +..|-+|.|.+.-+|++||.+ ||..|+|.. |-|....
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~------ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPS------NGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecCC------CCceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecC
Confidence            56788888887655 57888999999998776553      445899999999999999996 999998754 4565544


Q ss_pred             CC
Q 005812          295 PK  296 (676)
Q Consensus       295 ~~  296 (676)
                      .+
T Consensus       269 Dk  270 (350)
T KOG4285|consen  269 DK  270 (350)
T ss_pred             CH
Confidence            43

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=90.38  E-value=2.5  Score=36.18  Aligned_cols=67  Identities=15%  Similarity=0.211  Sum_probs=49.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccC-CceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPV-GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG  284 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~-G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~  284 (676)
                      ...+.+-..|..++.++|..+.+.+ ..|..++|+++.  ..++--+++.|.+.++|......+||+.|.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            3445555556666667777666664 347788998863  235667999999999999999999999873

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=90.21  E-value=0.96  Score=48.52  Aligned_cols=58  Identities=16%  Similarity=0.280  Sum_probs=49.0

Q ss_pred             CeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHc
Q 005812          578 TRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLN  655 (676)
Q Consensus       578 ~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~ln  655 (676)
                      |.|.+|-||..+..++++.||...       .+..+.+|.+-.+             .-.||.|.+..||++|+..|.
T Consensus       176 cIvilREIpettp~e~Vk~lf~~e-------ncPk~iscefa~N-------------~nWyITfesd~DAQqAykylr  233 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGE-------NCPKVISCEFAHN-------------DNWYITFESDTDAQQAYKYLR  233 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccC-------CCCCceeeeeeec-------------CceEEEeecchhHHHHHHHHH
Confidence            679999999999999999999842       4678888888644             357999999999999988773

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=89.55  E-value=1  Score=39.64  Aligned_cols=66  Identities=20%  Similarity=0.300  Sum_probs=47.6

Q ss_pred             CcEEEEcCCCcc----ccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCe
Q 005812          121 ARTVIIGGLLNA----DMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKE  196 (676)
Q Consensus       121 ~~~l~V~nLp~~----~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~  196 (676)
                      -.||.|.=|...    -+...+....+.||+|.+|.+.                .+..|.|.|.+..+|.+|+.++.. .
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c----------------GrqsavVvF~d~~SAC~Av~Af~s-~  148 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC----------------GRQSAVVVFKDITSACKAVSAFQS-R  148 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec----------------CCceEEEEehhhHHHHHHHHhhcC-C
Confidence            347777655444    4455566778899999999943                345699999999999999998766 3


Q ss_pred             ecCeEEE
Q 005812          197 IKGGTVW  203 (676)
Q Consensus       197 ~~~~~i~  203 (676)
                      ..|..+.
T Consensus       149 ~pgtm~q  155 (166)
T PF15023_consen  149 APGTMFQ  155 (166)
T ss_pred             CCCceEE
Confidence            3444443

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=89.52  E-value=0.71  Score=43.55  Aligned_cols=62  Identities=19%  Similarity=0.247  Sum_probs=46.0

Q ss_pred             CHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhC--CceeCCeeEEEEEecCC
Q 005812          229 KVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN--GQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       229 ~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~--~~~~~g~~i~v~~a~~~  296 (676)
                      ..+.|+.+|..|+.+......+.      -+-..|.|.+.+.|.+|...|+  +..+.|..++|.++.+.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            34789999999999888877763      2448999999999999999999  89999999999998543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=89.39  E-value=2.7  Score=35.96  Aligned_cols=66  Identities=15%  Similarity=0.186  Sum_probs=48.3

Q ss_pred             CeEEEecC-CcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcC
Q 005812          578 TRLVIYNL-PKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN  656 (676)
Q Consensus       578 ~~l~V~nl-p~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng  656 (676)
                      +.|.|--. |..++-++|..+...        .-..|..++|+++..        .++=.+.+.|.++++|..=...+||
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~--------~~~~i~~~riird~~--------pnrymVLikF~~~~~Ad~Fy~~fNG   76 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAP--------FREDIEHIRIIRDGT--------PNRYMVLIKFRDQESADEFYEEFNG   76 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhc--------ccccEEEEEEeeCCC--------CceEEEEEEECCHHHHHHHHHHhCC
Confidence            44444444 445555666555443        245788899998842        5678999999999999999999999


Q ss_pred             CCC
Q 005812          657 NPS  659 (676)
Q Consensus       657 ~~~  659 (676)
                      .+.
T Consensus        77 k~F   79 (110)
T PF07576_consen   77 KPF   79 (110)
T ss_pred             Ccc
Confidence            987

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=88.93  E-value=1.6  Score=33.50  Aligned_cols=55  Identities=16%  Similarity=0.322  Sum_probs=42.9

Q ss_pred             CCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          227 KAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       227 ~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      .++-++++..+..|+-. +|.  .+     ..|| ||.|.+..+|++|....+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~-~I~--~d-----~tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD-RIR--DD-----RTGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcc-eEE--ec-----CCEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            46778999999999743 233  33     2354 99999999999999999999988777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=88.70  E-value=2.1  Score=32.82  Aligned_cols=55  Identities=15%  Similarity=0.247  Sum_probs=43.3

Q ss_pred             CCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          436 DLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       436 ~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++-++++..+..|+- ..  |..++     .|| ||.|.+..+|.++....+     |..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~--I~~d~-----tGf-YIvF~~~~Ea~rC~~~~~-----~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DR--IRDDR-----TGF-YIVFNDSKEAERCFRAED-----GTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ce--EEecC-----CEE-EEEECChHHHHHHHHhcC-----CCEEEEEEEEe
Confidence            4788999999999973 23  33332     455 899999999999999999     88888877665

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=88.52  E-value=0.45  Score=52.25  Aligned_cols=72  Identities=18%  Similarity=0.152  Sum_probs=62.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ..++..++||+|+-..+..+-++.+...+|.|.++...         -|||..|..+..+.+|+..++     ...++|.
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~---------~fgf~~f~~~~~~~ra~r~~t-----~~~~~~~  101 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRD---------KFGFCEFLKHIGDLRASRLLT-----ELNIDDQ  101 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhh---------hhcccchhhHHHHHHHHHHhc-----ccCCCcc
Confidence            44456799999999999999999999999999887543         189999999999999999999     7888888


Q ss_pred             EEEEEE
Q 005812          501 QLTVLK  506 (676)
Q Consensus       501 ~l~v~~  506 (676)
                      .+.+..
T Consensus       102 kl~~~~  107 (668)
T KOG2253|consen  102 KLIENV  107 (668)
T ss_pred             hhhccc
Confidence            887755

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=88.42  E-value=0.33  Score=51.03  Aligned_cols=74  Identities=22%  Similarity=0.309  Sum_probs=59.1

Q ss_pred             CCCeEEEcCCCCCC-CHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          424 LQNTIFICNLPFDL-DNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       424 ~~~~l~V~nLp~~~-teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      ..+.|-+.-.|+.. +..+|..+|.+||.|..|.+-.      +.-.|.|+|.+..+|-+|-+ .+     +..|++|.|
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~------~~~~a~vTF~t~aeag~a~~-s~-----~avlnnr~i  438 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDY------SSLHAVVTFKTRAEAGEAYA-SH-----GAVLNNRFI  438 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccC------chhhheeeeeccccccchhc-cc-----cceecCcee
Confidence            34566677777766 5789999999999999986532      24468999999999977764 45     899999999


Q ss_pred             EEEEccC
Q 005812          503 TVLKALD  509 (676)
Q Consensus       503 ~v~~a~~  509 (676)
                      +|.|-.+
T Consensus       439 Kl~whnp  445 (526)
T KOG2135|consen  439 KLFWHNP  445 (526)
T ss_pred             EEEEecC
Confidence            9999766

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=88.13  E-value=0.29  Score=51.44  Aligned_cols=76  Identities=21%  Similarity=0.370  Sum_probs=61.9

Q ss_pred             CcEEEEcCCCCCC-CHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          216 KWKLIIRNIPFKA-KVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       216 ~~~v~V~nLp~~~-~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      .+.+-+.-.|+.+ +-++|..+|.+||.|..|.+-..      .-.|.|+|.+..+|-.|.. .++..|.++.|+|.|..
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whn  444 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHN  444 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEEec
Confidence            4556666667665 46899999999999999988664      2349999999999988877 48999999999999998


Q ss_pred             CCCC
Q 005812          295 PKNI  298 (676)
Q Consensus       295 ~~~~  298 (676)
                      +...
T Consensus       445 ps~~  448 (526)
T KOG2135|consen  445 PSPV  448 (526)
T ss_pred             CCcc
Confidence            8553

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=86.45  E-value=2.2  Score=42.45  Aligned_cols=65  Identities=15%  Similarity=0.135  Sum_probs=50.3

Q ss_pred             CcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCe
Q 005812          121 ARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGG  200 (676)
Q Consensus       121 ~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~  200 (676)
                      ..-|-|-++|+.... -|..+|..||+|.+...               +.+-.+-+|.|.+.-+|.+||. .||+.|.|.
T Consensus       197 D~WVTVfGFppg~~s-~vL~~F~~cG~Vvkhv~---------------~~ngNwMhirYssr~~A~KALs-kng~ii~g~  259 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQVS-IVLNLFSRCGEVVKHVT---------------PSNGNWMHIRYSSRTHAQKALS-KNGTIIDGD  259 (350)
T ss_pred             cceEEEeccCccchh-HHHHHHHhhCeeeeeec---------------CCCCceEEEEecchhHHHHhhh-hcCeeeccc
Confidence            345777788776543 47789999999998872               2445678999999999999998 588888876


Q ss_pred             EE
Q 005812          201 TV  202 (676)
Q Consensus       201 ~i  202 (676)
                      .+
T Consensus       260 vm  261 (350)
T KOG4285|consen  260 VM  261 (350)
T ss_pred             eE
Confidence            54

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=84.49  E-value=1.2  Score=36.31  Aligned_cols=64  Identities=14%  Similarity=0.105  Sum_probs=44.3

Q ss_pred             EEEEeCCHHHHHHHHHHh-CCCeecCeEEEEecCC--C-------CCCCCCCcEEEEcCCCCCCCHHHHHHhhc
Q 005812          175 SAVLYTTVKSACASVALL-HQKEIKGGTVWARQLG--G-------EGSKTQKWKLIIRNIPFKAKVNEIKDMFS  238 (676)
Q Consensus       175 afV~F~~~~~A~~A~~~l-~~~~~~~~~i~v~~~~--~-------~~~~~~~~~v~V~nLp~~~~e~~l~~~F~  238 (676)
                      |+|.|..+.-|+.-+..- +.-.+.+..+.++..+  .       -....+.++|.|.|||..+++++|++.++
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeEE
Confidence            689999999999988732 2234455555443221  1       11346778999999999999999987543

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=83.50  E-value=3.5  Score=43.37  Aligned_cols=67  Identities=21%  Similarity=0.305  Sum_probs=58.4

Q ss_pred             CCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcC
Q 005812          577 RTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN  656 (676)
Q Consensus       577 ~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng  656 (676)
                      .+.|+|-.+|..+|-.||..|+..+        .-.|..++|+||..        +.+=..++.|.+.++|..-...+||
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~--------~~~I~~irivRd~~--------pnrymvLIkFr~q~da~~Fy~efNG  137 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASF--------IKQISDIRIVRDGM--------PNRYMVLIKFRDQADADTFYEEFNG  137 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHH--------hhhhheeEEeecCC--------CceEEEEEEeccchhHHHHHHHcCC
Confidence            4679999999999999999999863        45688899999753        5677899999999999999999999


Q ss_pred             CCC
Q 005812          657 NPS  659 (676)
Q Consensus       657 ~~~  659 (676)
                      .+.
T Consensus       138 k~F  140 (493)
T KOG0804|consen  138 KQF  140 (493)
T ss_pred             CcC
Confidence            865

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=82.94  E-value=1.3  Score=36.19  Aligned_cols=33  Identities=18%  Similarity=0.190  Sum_probs=25.0

Q ss_pred             EEEEecCHHHHHHHHHHhCCc-eecCeEEEEeec
Q 005812           14 GYVQFAVMEDANRAVEMKNGT-SVGGRKIGVKHA   46 (676)
Q Consensus        14 afV~F~~~edA~~Al~~~~g~-~i~gr~i~v~~a   46 (676)
                      |+|+|..++=|++-++.-... .+.+..++|..+
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~   34 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVS   34 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEE
Confidence            789999999999999883333 566777777554

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=81.67  E-value=4.1  Score=38.51  Aligned_cols=63  Identities=22%  Similarity=0.268  Sum_probs=43.9

Q ss_pred             CHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccC
Q 005812          438 DNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALD  509 (676)
Q Consensus       438 teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~  509 (676)
                      ..+.|+++|..|+.+..+.+++.      -+-..|.|.+.++|.+|...|+..   +..+.|..+.|.++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~---~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWD---GTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST-----TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhccc---ccccCCCceEEEEccc
Confidence            45789999999999888766533      345789999999999999997621   5789999999999854

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=80.35  E-value=5.7  Score=41.91  Aligned_cols=68  Identities=12%  Similarity=0.159  Sum_probs=58.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCC-ceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFG-EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G-~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      +..|+|-.+|..++--||..|+..|- .|..++|++|..  ..+-.++|.|.+..+|......+|     |..|..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efN-----Gk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFN-----GKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcC-----CCcCCC
Confidence            68999999999999999999999864 688899998642  234568999999999999999999     888864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	676
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-09
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-06
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		1e-09
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		1e-06
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		1e-08
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		2e-08
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		2e-07
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		3e-07
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		3e-07
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		3e-07
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		3e-07
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		3e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		4e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		5e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		5e-07
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		5e-07
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		7e-07
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		1e-06
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		2e-06
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		3e-06
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		3e-06
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		4e-06
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		1e-05
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		2e-05
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-05
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-05
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		2e-05
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		2e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-05
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		3e-05
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		3e-05
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		3e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		3e-05
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		3e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		5e-05
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		5e-05
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-04
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		1e-04
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		1e-04
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		2e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		2e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		2e-04
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		2e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		3e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		3e-04
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		3e-04
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		5e-04
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		5e-04
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		6e-04
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		6e-04
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		7e-04
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		7e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		8e-04

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 51/175 (29%), Positives = 79/175 (45%), Gaps = 12/175 (6%)
Query: 122 RTVIIGGLLNADMAE-EVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYT 180
           RT +I   L  +M + E+  L  SIG V S    L ++++  H L           V Y 
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAK--LIRDKVAGHSLGY-------GFVNYV 52
Query: 181 TVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPV 240
           T K A  ++  L+   ++  T+            +   L I  +P      +++DMFS  
Sbjct: 53  TAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRF 112
Query: 241 GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK--FGKRPIAVDWA 293
           G + N  +  +  TGLS+G AF++F  + +AE AI  FNG K      PI V +A
Sbjct: 113 GRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVKFA 167

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           +  LI+  +P     +E++ +FS +G V +  +  +   G S G+ FV +   +DAE AI
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 276 QKFNGQKFGKRPIAVDWAVPK-------NIYSSG 302
              NG +   + I V +A P        N+Y SG
Sbjct: 62  NTLNGLRLQSKTIKVSYARPSSEVIKDANLYISG 95

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 51/175 (29%), Positives = 79/175 (45%), Gaps = 12/175 (6%)
Query: 122 RTVIIGGLLNADMAE-EVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYT 180
           RT +I   L  +M + E+  L  SIG V S    L ++++  H L           V Y 
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAK--LIRDKVAGHSLGY-------GFVNYV 52
Query: 181 TVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPV 240
           T K A  ++  L+   ++  T+            +   L I  +P      +++DMFS  
Sbjct: 53  TAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRF 112
Query: 241 GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK--FGKRPIAVDWA 293
           G + N  +  +  TGLS+G AF++F  + +AE AI  FNG K      PI V +A
Sbjct: 113 GRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVXFA 167

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           +  LI+  +P     +E++ +FS +G V +  +  +   G S G+ FV +   +DAE AI
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 276 QKFNGQKFGKRPIAVDWAVPK-------NIYSSG 302
              NG +   + I V +A P        N+Y SG
Sbjct: 62  NTLNGLRLQSKTIKVSYARPSSEVIKDANLYISG 95

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 48/79 (60%), Gaps = 4/79 (5%)
Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHN-TDTGLSKGFAFVKFTCKRDAESAIQ 276
           K+++RNIPF+A   EI+++FS  G +  V +P   T TG  +GF FV F  K+DA+ A  
Sbjct: 17  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76
Query: 277 KF--NGQKFGKRPIAVDWA 293
               +   +G+R + ++WA
Sbjct: 77  ALCHSTHLYGRR-LVLEWA 94

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 232 EIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD 291
           +IK  F+P G + +  +  +  TG SKG+ FV F  K DAE+AIQ+  GQ  G R I  +
Sbjct: 31  DIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN 90
Query: 292 WAV-----PKNIYSS 301
           WA      PK+ Y S
Sbjct: 91  WATRKPPAPKSTYES 105

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/84 (28%), Positives = 46/84 (54%)
Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
           G     + W L +  +  +A   +I D F+  G + N+++  +  TG  KG+  V++   
Sbjct: 2   GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
Query: 269 RDAESAIQKFNGQKFGKRPIAVDW 292
           ++A++A++  NGQ    +PI+VDW
Sbjct: 62  KEAQAAMEGLNGQDLMGQPISVDW 85

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 24/84 (28%), Positives = 46/84 (54%)
Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
           G     + W L +  +  +A   +I D F+  G + N+++  +  TG  KG+  V++   
Sbjct: 16  GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 75
Query: 269 RDAESAIQKFNGQKFGKRPIAVDW 292
           ++A++A++  NGQ    +PI+VDW
Sbjct: 76  KEAQAAMEGLNGQDLMGQPISVDW 99

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 23/78 (29%), Positives = 45/78 (57%)
Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           + W L +  +  +A   +I D F+  G + N+++  +  TG  KG+  V++   ++A++A
Sbjct: 6   EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 275 IQKFNGQKFGKRPIAVDW 292
           ++  NGQ    +PI+VDW
Sbjct: 66  MEGLNGQDLMGQPISVDW 83

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 24/84 (28%), Positives = 46/84 (54%)
Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
           G     + W L +  +  +A   +I D F+  G + N+++  +  TG  KG+  V++   
Sbjct: 15  GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
Query: 269 RDAESAIQKFNGQKFGKRPIAVDW 292
           ++A++A++  NGQ    +PI+VDW
Sbjct: 75  KEAQAAMEGLNGQDLMGQPISVDW 98

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 23/78 (29%), Positives = 45/78 (57%)
Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           + W L +  +  +A   +I D F+  G + N+++  +  TG  KG+  V++   ++A++A
Sbjct: 6   EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 275 IQKFNGQKFGKRPIAVDW 292
           ++  NGQ    +PI+VDW
Sbjct: 66  MEGLNGQDLMGQPISVDW 83

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 23/78 (29%), Positives = 45/78 (57%)
Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           + W L +  +  +A   +I D F+  G + N+++  +  TG  KG+  V++   ++A++A
Sbjct: 6   EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 275 IQKFNGQKFGKRPIAVDW 292
           ++  NGQ    +PI+VDW
Sbjct: 66  MEGLNGQDLMGQPISVDW 83

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 26/75 (34%), Positives = 47/75 (62%)
Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           + + NIP++A   ++KD+FS VG V +  + ++ +TG  KG+ F ++  +  A SA++  
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 279 NGQKFGKRPIAVDWA 293
           NG++F  R + VD A
Sbjct: 71  NGREFSGRALRVDNA 85

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 20/53 (37%), Positives = 32/53 (60%)
Query: 422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKF 474
           D    ++F+ N+P++   E++K  FS  G VVSF  V  + T +PKG GF ++
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEY 57

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 53.1 bits (126), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 208 GGEGSKTQK------WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFA 261
           G  GS  QK      + + + ++  +    +IK  F+P G + +  +  +  TG SKG+ 
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
Query: 262 FVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSG 302
           FV F  K DAE+AI    GQ  G R I  +WA  K    SG
Sbjct: 61  FVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKPPAPSG 101

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 53.1 bits (126), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 27/88 (30%), Positives = 48/88 (54%), Gaps = 3/88 (3%)
Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           W L + +I  +A+ +EI++ F   G + N+++  +  TG SKG+A V++   + A +A +
Sbjct: 73  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132
Query: 277 KFNGQKFGKRPIAVDWAV---PKNIYSS 301
             NG +   + I VDW     PK +  S
Sbjct: 133 ALNGAEIMGQTIQVDWCFVKGPKRVKKS 160

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 27/75 (36%), Positives = 42/75 (56%)
Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+ ++   + ++ +F   G V +VYIP +  T  S+GFAFV+F  KRDAE A+   
Sbjct: 50  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 279 NGQKFGKRPIAVDWA 293
           +G     R + V  A
Sbjct: 110 DGAVLDGRELRVQMA 124

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 47/88 (53%)
Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
           G     + W L + +I  +A+ +EI++ F   G + N+++  +  TG SKG+A V++   
Sbjct: 19  GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 269 RDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           + A +A +  NG +   + I VDW   K
Sbjct: 79  KQALAAKEALNGAEIMGQTIQVDWCFVK 106

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/75 (36%), Positives = 42/75 (56%)
Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+ ++   + ++ +F   G V +VYIP +  T  S+GFAFV+F  KRDAE A+   
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 279 NGQKFGKRPIAVDWA 293
           +G     R + V  A
Sbjct: 133 DGAVLDGRELRVQMA 147

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 25/58 (43%), Positives = 33/58 (56%)
Query: 239 PVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           P G + +  +  +  TG SKG+ FV F  K DAE+AIQ+  GQ  G R I  +WA  K
Sbjct: 29  PFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 25/87 (28%), Positives = 47/87 (54%), Gaps = 3/87 (3%)
Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           + N+    +  +++++F P G +  +Y+  +  TG SKGFAF+ F  + DA  AI   +G
Sbjct: 20  VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 281 QKFGKRPIAVDWAVPKNIYSSGGAAAG 307
             +    + V+WA P    ++ G ++G
Sbjct: 80  FGYDHLILNVEWAKPS---TNSGPSSG 103

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 235 DMFSPVGLVWNV-YIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA 293
           D FS  G++     I  + DTG SKG+AF+ F     +++AI+  NGQ    RPI V +A
Sbjct: 24  DTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA 83
Query: 294 VPKNIYSSGGAAA 306
             K+   SG ++ 
Sbjct: 84  FKKDSKGSGPSSG 96

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 25/81 (30%), Positives = 41/81 (50%)
Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           Q   LI+  +P     +E++ +FS +G V +  +  +   G S G+ FV +   +DAE A
Sbjct: 18  QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 275 IQKFNGQKFGKRPIAVDWAVP 295
           I   NG +   + I V +A P
Sbjct: 78  INTLNGLRLQSKTIKVSYARP 98

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/116 (26%), Positives = 58/116 (50%), Gaps = 6/116 (5%)
Query: 183 KSACASVAL--LHQKEIKGGTV---WARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMF 237
           +S  A++AL  L+ K+I+   V   WA Q   + S    + L + ++        +++ F
Sbjct: 50  QSHDANIALQTLNGKQIENNIVKINWAFQ-SQQSSSDDTFNLFVGDLNVNVDDETLRNAF 108
Query: 238 SPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA 293
                  + ++  +  TG S+G+ FV FT + DA++A+    GQ    RP+ ++WA
Sbjct: 109 KDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 40/77 (51%)
Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           LI+  +P     +E++ +FS +G V +  +  +   G S G+ FV +   +DAE AI   
Sbjct: 7   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 279 NGQKFGKRPIAVDWAVP 295
           NG +   + I V +A P
Sbjct: 67  NGLRLQSKTIKVSYARP 83

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/94 (30%), Positives = 45/94 (47%), Gaps = 7/94 (7%)
Query: 216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           K  LI+  +P     +E K +F  +G + +  +  +  TG S G+ FV ++   DA+ AI
Sbjct: 4   KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 276 QKFNGQKFGKRPIAVDWAVPK-------NIYSSG 302
              NG K   + I V +A P        N+Y SG
Sbjct: 64  NTLNGLKLQTKTIKVSYARPSSASIRDANLYVSG 97

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 45/85 (52%), Gaps = 2/85 (2%)
Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDA 271
           +K+Q  +L + NIPF+ +  +++ MF   G + +V I  N     SKGF FV F    DA
Sbjct: 25  NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADA 82
Query: 272 ESAIQKFNGQKFGKRPIAVDWAVPK 296
           + A +K +G     R I V+ A  +
Sbjct: 83  DRAREKLHGTVVEGRKIEVNNATAR 107

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/75 (32%), Positives = 40/75 (53%)
Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+ ++   + ++ +F   G V +VYIP    T   +GFAFV+F  +RDA+ A    
Sbjct: 16  LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 279 NGQKFGKRPIAVDWA 293
           +G +   R + V  A
Sbjct: 76  DGAELDGRELRVQVA 90

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 21/72 (29%), Positives = 41/72 (56%)
Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + ++ F    + ++ +F P G + N+ +  ++DTG SKG+ F+ F+    A  A+++ 
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 279 NGQKFGKRPIAV 290
           NG +   RP+ V
Sbjct: 68  NGFELAGRPMRV 79

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 30/99 (30%), Positives = 46/99 (46%)
Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G  G  T K  L +  +  +     +   F P G + ++ IP + +T   +GFAFV+F  
Sbjct: 4   GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 63
Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAA 306
             DA +AI   N  +   R I V+ A P  I  SG ++ 
Sbjct: 64  AEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESGPSSG 102

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/86 (33%), Positives = 45/86 (52%), Gaps = 7/86 (8%)
Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           +IP+     +I D+ S VG V N+ +  +  TG SKG+AF++F     + SA++  NG +
Sbjct: 9   SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 68
Query: 283 FGKRPIAVDWAVPKNIYSSGGAAAGV 308
            G R +       K  YSS    +GV
Sbjct: 69  LGSRFL-------KCGYSSNSDISGV 87

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/86 (33%), Positives = 45/86 (52%), Gaps = 7/86 (8%)
Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           +IP+     +I D+ S VG V N+ +  +  TG SKG+AF++F     + SA++  NG +
Sbjct: 10  SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 69
Query: 283 FGKRPIAVDWAVPKNIYSSGGAAAGV 308
            G R +       K  YSS    +GV
Sbjct: 70  LGSRFL-------KCGYSSNSDISGV 88

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/94 (29%), Positives = 44/94 (46%), Gaps = 7/94 (7%)
Query: 216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           K  LI+  +P      E + +F  +G + +  +  +  TG S G+ FV +   +DAE AI
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 276 QKFNGQKFGKRPIAVDWAVPK-------NIYSSG 302
              NG +   + I V +A P        N+Y SG
Sbjct: 62  NTLNGLRLQTKTIKVSYARPSSASIRDANLYVSG 95

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 23/64 (35%), Positives = 37/64 (57%)
Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           +IP+     +I D+ S VG V N+ +  +  TG SKG+AF++F     + SA++  NG +
Sbjct: 11  SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 70
Query: 283 FGKR 286
            G R
Sbjct: 71  LGSR 74

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 25/82 (30%), Positives = 41/82 (50%)
Query: 216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           K  LI+  +P     +E K +F  +G + +  +  +  TG S G+ FV ++   DA+ AI
Sbjct: 4   KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 276 QKFNGQKFGKRPIAVDWAVPKN 297
              NG K   + I V +A P +
Sbjct: 64  NTLNGLKLQTKTIKVSYARPSS 85

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/89 (32%), Positives = 47/89 (52%), Gaps = 2/89 (2%)
Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L + NIPF+ +  +++ MF   G + +V I  N     SKGF FV F    DA+ A +K
Sbjct: 17  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 74
Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGGAAA 306
            +G     R I V+ A  + + +SG ++ 
Sbjct: 75  LHGTVVEGRKIEVNNATARVMTNSGPSSG 103

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 39/80 (48%)
Query: 214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAES 273
           + + KL +  + F      ++ +FS  G +  V +  + +T  S+GF FV F    DA+ 
Sbjct: 10  SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 274 AIQKFNGQKFGKRPIAVDWA 293
           A+   NG+    R I VD A
Sbjct: 70  AMMAMNGKSVDGRQIRVDQA 89

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 17/43 (39%), Positives = 27/43 (62%)
Query: 251 NTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA 293
           +  TG S+G+ FV FT + DA++A+    GQ    RP+ ++WA
Sbjct: 36  DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 78

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/73 (26%), Positives = 43/73 (58%)
Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L + ++ F    + ++ +F P G + ++ +  +++TG SKG+ F+ F+    A+ A+++
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 278 FNGQKFGKRPIAV 290
            NG +   RP+ V
Sbjct: 88  LNGFELAGRPMKV 100

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 39/77 (50%)
Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           LI+  +P      E+  +F  +G +    I  +  TG S G+AFV FT + D++ AI+  
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 279 NGQKFGKRPIAVDWAVP 295
           NG     + + V +A P
Sbjct: 66  NGITVRNKRLKVSYARP 82

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 39/77 (50%)
Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           LI+  +P      E+  +F  +G +    I  +  TG S G+AFV FT + D++ AI+  
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 279 NGQKFGKRPIAVDWAVP 295
           NG     + + V +A P
Sbjct: 66  NGITVRNKRLKVSYARP 82

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/65 (33%), Positives = 40/65 (61%)
Query: 232 EIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD 291
           +++++FS  G + +V I ++  +  S+GFAFV F    DA+ A ++ NG +   R I VD
Sbjct: 28  DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 87
Query: 292 WAVPK 296
           +++ K
Sbjct: 88  FSITK 92

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/90 (28%), Positives = 46/90 (51%)
Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L +RN+ + +   +++ +FS  G +  ++ P ++ T   KGFAFV F     A  A  +
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGGAAAG 307
            +GQ F  R + V  +  K   S  G ++G
Sbjct: 70  VDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/107 (26%), Positives = 52/107 (48%), Gaps = 3/107 (2%)
Query: 193 HQKEIKGGTVW---ARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIP 249
           H   + GG      +R +G   +      L +  +       +++++FS  G + +V I 
Sbjct: 20  HMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIV 79
Query: 250 HNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           ++  +  S+GFAFV F    DA+ A ++ NG +   R I VD+++ K
Sbjct: 80  YDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 39/77 (50%)
Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           LI+  +P      E+  +F  +G +    I  +  TG S G+AFV FT + D++ AI+  
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 279 NGQKFGKRPIAVDWAVP 295
           NG     + + V +A P
Sbjct: 77  NGITVRNKRLKVSYARP 93

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/65 (33%), Positives = 40/65 (61%)
Query: 232 EIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD 291
           +++++FS  G + +V I ++  +  S+GFAFV F    DA+ A ++ NG +   R I VD
Sbjct: 31  DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 90
Query: 292 WAVPK 296
           +++ K
Sbjct: 91  FSITK 95

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           + + N+ + A   ++K++FS  G V+NV + ++ +T   KGF FV+   +  +E AI K 
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAKL 62
Query: 279 NGQKFGKRPIAVDWAVPK 296
           +   F  R I V  A PK
Sbjct: 63  DNTDFMGRTIRVTEANPK 80

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 29/48 (60%)
Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFT 266
           LI+  +P+K    ++K+ FS  G V  V +  +  TG SKGF FV+FT
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT 65

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 53/111 (47%), Gaps = 7/111 (6%)
Query: 192 LHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHN 251
           L Q+ I  G   +++ G EG+      L I ++P +    ++  MF P G V +  +  +
Sbjct: 8   LTQQSI--GAAGSQKEGPEGAN-----LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60
Query: 252 TDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSG 302
             T LSK F FV +     A++AIQ  NG + G + + V     KN   SG
Sbjct: 61  KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSG 111

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/106 (23%), Positives = 47/106 (44%), Gaps = 6/106 (5%)
Query: 187 ASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNV 246
           A++   HQ  ++      R+L  +   T    L + N+P      + +++  P G +   
Sbjct: 72  AAINAFHQSRLR-----ERELSVQLQPTDAL-LCVANLPPSLTQQQFEELVRPFGSLERC 125
Query: 247 YIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW 292
           ++ ++  TG SKG+ F ++  K  A  A     G+  G R + V W
Sbjct: 126 FLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW 171

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/106 (23%), Positives = 47/106 (44%), Gaps = 6/106 (5%)
Query: 187 ASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNV 246
           A++   HQ  ++      R+L  +   T    L + N+P      + +++  P G +   
Sbjct: 72  AAINAFHQSRLR-----ERELSVQLQPTDAL-LCVANLPPSLTQQQFEELVRPFGSLERC 125
Query: 247 YIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW 292
           ++ ++  TG SKG+ F ++  K  A  A     G+  G R + V W
Sbjct: 126 FLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW 171

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/106 (23%), Positives = 47/106 (44%), Gaps = 6/106 (5%)
Query: 187 ASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNV 246
           A++   HQ  ++      R+L  +   T    L + N+P      + +++  P G +   
Sbjct: 70  AAINAFHQSRLR-----ERELSVQLQPTDAL-LCVANLPPSLTQQQFEELVRPFGSLERC 123
Query: 247 YIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW 292
           ++ ++  TG SKG+ F ++  K  A  A     G+  G R + V W
Sbjct: 124 FLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW 169

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 42.4 bits (98), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +  +P      E++ +FS  G +    I  +  TG+S+G  F++F  + +AE AI+  
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 279 NGQK--FGKRPIAVDWA 293
           NGQK      PI V +A
Sbjct: 64  NGQKPLGAAEPITVKFA 80

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	676
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-27
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-11
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-08
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-06
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-06
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-05
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-04
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-26
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-14
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-08
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	7e-23
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-18
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-06
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	5e-22
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	8e-16
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	8e-07
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	5e-22
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-12
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-06
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	6e-22
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-14
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-06
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	8e-22
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-05
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-04
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-22
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-16
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-07
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-21
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-15
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	5e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-21
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-14
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-08
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-20
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	6e-14
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-20
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	7e-11
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-20
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-10
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	8e-07
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-20
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-15
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-20
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-12
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-20
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-10
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-20
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-04
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-04
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-19
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-16
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-09
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-19
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	9e-14
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-19
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-18
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-04
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-19
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	7e-16
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-08
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-19
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-15
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-07
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-19
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-14
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-08
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-19
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-15
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-06
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	5e-19
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-14
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	7e-08
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-19
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	6e-12
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-05
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-04
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	8e-19
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-16
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-13
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-12
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-07
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-04
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-18
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-12
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	7e-08
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-18
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	9e-15
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-08
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-18
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-14
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	9e-07
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-18
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-09
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-05
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-18
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-12
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-08
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-18
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-16
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-13
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-07
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-07
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-18
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-12
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-07
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-18
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	7e-12
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	5e-05
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	5e-04
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-18
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-14
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-09
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	8e-04
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-18
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-11
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-06
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-18
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-14
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	9e-09
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-18
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-11
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	6e-08
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-18
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-12
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-07
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-18
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-14
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-13
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-12
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	8e-08
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-18
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-12
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-08
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	8e-18
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-11
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	8e-05
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-18
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-17
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	7e-09
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-04
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-17
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-13
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	6e-08
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-17
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-12
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	9e-08
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-17
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-12
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	5e-06
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	7e-12
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-08
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-17
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-10
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-17
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-10
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-05
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-17
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-08
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-17
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-16
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-16
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-15
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-10
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-07
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	7e-17
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	6e-09
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-04
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	8e-17
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	8e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-06
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-16
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-14
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-09
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-06
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-06
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-16
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	5e-08
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-16
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-11
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-16
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-11
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-04
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-16
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-07
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-16
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-04
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-16
2dis_A	109	Unnamed protein product; structural genomics, RRM	5e-12
2dis_A	109	Unnamed protein product; structural genomics, RRM	9e-07
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-16
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	5e-12
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	7e-06
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-16
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-10
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	8e-08
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-16
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-13
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-16
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-04
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-16
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-12
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	9e-05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-16
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	7e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	6e-05
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-16
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-14
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-06
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-16
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-08
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-06
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-16
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-13
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-16
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-11
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-16
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-10
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-04
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	6e-16
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-15
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-06
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	8e-16
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-11
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-07
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	9e-16
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	9e-13
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-08
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-15
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-08
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	7e-06
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-15
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-15
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-05
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-15
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-15
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	5e-11
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-07
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-15
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-06
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	9e-06
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-15
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-15
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-04
2div_A	99	TRNA selenocysteine associated protein; structural	2e-15
2div_A	99	TRNA selenocysteine associated protein; structural	3e-09
2div_A	99	TRNA selenocysteine associated protein; structural	1e-04
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-15
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-08
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-15
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-06
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-06
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-15
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-10
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-05
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-15
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-10
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-06
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-15
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-07
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-06
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	3e-15
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	7e-11
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-05
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-15
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-14
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-11
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-07
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-06
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-15
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	9e-12
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-15
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-12
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-06
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-15
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-13
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-08
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-15
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-07
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-06
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-15
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-10
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-15
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-05
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-15
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-15
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-13
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-15
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-12
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-04
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	7e-15
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-06
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-06
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	8e-15
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-12
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-07
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-14
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-09
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	8e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-14
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-12
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	5e-07
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	6e-07
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	6e-06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-14
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	4e-12
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-07
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-14
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-09
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-04
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-14
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-12
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-07
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-14
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	9e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-07
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-14
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-12
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	6e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-14
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-14
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	5e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-04
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	6e-14
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-05
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-14
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	9e-14
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	8e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	9e-14
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	7e-10
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	7e-04
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-08
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	8e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-13
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-13
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-09
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	8e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-13
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-08
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	5e-04
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-13
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-08
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-13
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-07
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-13
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-08
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-13
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-13
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-05
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	9e-13
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	9e-13
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-09
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-04
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-12
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-09
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-12
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-07
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	7e-04
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-12
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-06
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-05
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-12
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-05
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-12
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	8e-10
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	8e-05
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-08
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	7e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-08
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	4e-12
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-07
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	5e-12
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	6e-12
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	6e-05
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	7e-12
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	5e-09
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	7e-12
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-08
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-06
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-11
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	3e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-04
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-05
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-09
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-11
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-04
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	7e-04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-11
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	6e-06
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	9e-05
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	6e-11
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-07
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	9e-05
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	7e-11
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-06
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	9e-04
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	7e-11
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	3e-06
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	8e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	6e-08
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	9e-11
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-10
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	7e-05
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	5e-04
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-10
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	7e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-04
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	6e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-10
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	7e-08
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	5e-10
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-06
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	5e-04
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	7e-10
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-05
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	8e-05
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	7e-10
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	7e-06
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	3e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-08
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-05
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-05
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	4e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-07
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	9e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-07
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	5e-07
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	5e-07
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	7e-07
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	2e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	9e-07
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	1e-06
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	2e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	7e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	9e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-05
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	3e-05
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-04
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	4e-04
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	5e-04

>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 Length = 292

 Score =  111 bits (279), Expect = 3e-27
 Identities = 47/302 (15%), Positives = 98/302 (32%), Gaps = 64/302 (21%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           ++++N+P     N++   F   G + +V +        +  FA ++F     A +AI K 
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITKT 101

Query: 279 NGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNS 338
           +    G+  I V       ++        + N                            
Sbjct: 102 HK-VVGQNEIIVSHLTECTLW--------MTN---------------------------- 124

Query: 339 SEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKG------NKEQDSDKT 392
                 P +      +   R +L  +     S+   S      +         ++D+   
Sbjct: 125 -----FPPSYT-QRNI---RDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 175

Query: 393 VNE-SAKVSDVSKLNSSKSKPKSLKQTEGEDELQN-TIFICNLPFDLDNEE-VKQRFSAF 449
           V + +    +   L +  S P    +      L+   I I NL  +L +E  +++ F  F
Sbjct: 176 VEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGF 235

Query: 450 GEVVS-FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKAL 508
           G +    +P   +         F+ F+  ++A  A+  +         L  R+++V  A 
Sbjct: 236 GSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMN------RSLLGNREISVSLAD 289

Query: 509 DK 510
            K
Sbjct: 290 KK 291

>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 Length = 292

 Score = 78.5 bits (194), Expect = 4e-16
 Identities = 32/189 (16%), Positives = 65/189 (34%), Gaps = 23/189 (12%)

Query: 110 DKEDCSQKQRVARTVIIGGLLNADMAEE-VHRLAGSIGTVCSVTYPLPKEELEQHGLAQE 168
              +   + R   TV++  L      +  V++     G +  V   +     +    A+ 
Sbjct: 30  KANEALTRNRELTTVLVKNL-PKSYNQNKVYKYFKHCGPIIHVD--VADSLKKNFRFAR- 85

Query: 169 GCKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKA 228
                   + +     A A++   H K +    +         S   +  L + N P   
Sbjct: 86  --------IEFARYDGALAAITKTH-KVVGQNEIIV-------SHLTECTLWMTNFPPSY 129

Query: 229 KVNEIKDMFSPVGLVW-NVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRP 287
               I+D+   + +V  ++ +P       S+ FA++  T K DA   ++K NG K     
Sbjct: 130 TQRNIRDLLQDINVVALSIRLPSL-RFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYT 188

Query: 288 IAVDWAVPK 296
           +    + P 
Sbjct: 189 LVTKVSNPL 197

>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 Length = 292

 Score = 78.1 bits (193), Expect = 5e-16
 Identities = 31/130 (23%), Positives = 59/130 (45%), Gaps = 12/130 (9%)

Query: 177 VLYTTVKSACASVALLHQKEIKGGTV---WARQLG----GEGSKTQKWKLIIRNIPFKAK 229
           +  T+ + A   V  L+  +I+G T+    +  L      + +  +  +++IRN+  +  
Sbjct: 164 IDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTEL- 222

Query: 230 VNE--IKDMFSPVGLVWNVYIPHN-TDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKR 286
           ++E  +++ F   G +  + IP    +   +   AF+ F  K  AE A+Q  N    G R
Sbjct: 223 LDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQM-NRSLLGNR 281

Query: 287 PIAVDWAVPK 296
            I+V  A  K
Sbjct: 282 EISVSLADKK 291

>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 Length = 292

 Score = 65.0 bits (159), Expect = 1e-11
 Identities = 28/238 (11%), Positives = 62/238 (26%), Gaps = 78/238 (32%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
            T+++ N P       ++        V   + +        +   ++   + E A   V 
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPA 545
                   G+ ++G  L    +        ++  ++ + T + R +              
Sbjct: 178 KLN-----GLKIEGYTLVTKVS-----NPLEKSKRTDSATLEGREIM------------- 214

Query: 546 AEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMT-EKGLKKLCIDAVVS 604
                                               I NL   +  E  L++        
Sbjct: 215 ------------------------------------IRNLSTELLDENLLRESF------ 232

Query: 605 RASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVAL----RVLNNNP 658
              +    I++I     +  G+ +    +   AF+ F     A  AL     +L N  
Sbjct: 233 ---EGFGSIEKIN----IPAGQKEHSF-NNCCAFMVFENKDSAERALQMNRSLLGNRE 282

>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 Length = 292

 Score = 53.1 bits (128), Expect = 9e-08
 Identities = 14/62 (22%), Positives = 22/62 (35%)

Query: 2   VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQ 61
           +     N  R F Y+     EDA   VE  NG  + G  +  K +      ++  S   +
Sbjct: 150 LPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLE 209

Query: 62  EV 63
             
Sbjct: 210 GR 211

>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 Length = 292

 Score = 48.8 bits (117), Expect = 2e-06
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
              +K  + +    ++ F   + A RA++M N + +G R+I V  A  +
Sbjct: 244 PAGQKEHSFNNCCAFMVFENKDSAERALQM-NRSLLGNREISVSLADKK 291

>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 Length = 292

 Score = 47.3 bits (113), Expect = 8e-06
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 15/83 (18%)

Query: 574 HVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYS 633
           H++   L + N P S T++ ++ L          +   V+     L SL+         S
Sbjct: 114 HLTECTLWMTNFPPSYTQRNIRDLL---------QDINVVALSIRLPSLRFNT------S 158

Query: 634 RGVAFVEFTEHQHALVALRVLNN 656
           R  A+++ T  + A   +  LN 
Sbjct: 159 RRFAYIDVTSKEDARYCVEKLNG 181

>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 Length = 292

 Score = 45.0 bits (107), Expect = 4e-05
 Identities = 24/114 (21%), Positives = 41/114 (35%), Gaps = 19/114 (16%)

Query: 543 TPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAV 602
            P ++   D+       L  KK  +  + N  +  T +++ NLPKS  +  + K      
Sbjct: 9   RPDSKRPLDEGSPAAAGLTSKKANEALTRNREL--TTVLVKNLPKSYNQNKVYKYFKHC- 65

Query: 603 VSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN 656
                     I  +    SLKK        +   A +EF  +  AL A+   + 
Sbjct: 66  --------GPIIHVDVADSLKK--------NFRFARIEFARYDGALAAITKTHK 103

>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 Length = 292

 Score = 43.4 bits (103), Expect = 1e-04
 Identities = 10/42 (23%), Positives = 18/42 (42%), Gaps = 1/42 (2%)

Query: 5   KGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
               ++  F  ++FA  + A  A+   +   VG  +I V H 
Sbjct: 75  DSLKKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVSHL 115

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score =  103 bits (259), Expect = 1e-26
 Identities = 33/101 (32%), Positives = 52/101 (51%), Gaps = 2/101 (1%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHN-TDTGLSKGFAFVKFT 266
           G    K    K+++RNIPF+A   EI+++FS  G +  V +P   T TG  +GF FV F 
Sbjct: 7   GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 66

Query: 267 CKRDAESAIQK-FNGQKFGKRPIAVDWAVPKNIYSSGGAAA 306
            K+DA+ A     +      R + ++WA  +    SG ++ 
Sbjct: 67  TKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSSG 107

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 69.3 bits (170), Expect = 1e-14
 Identities = 25/97 (25%), Positives = 44/97 (45%), Gaps = 5/97 (5%)

Query: 416 KQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS-FVPVLHQVTKRPKGTGFLKF 474
                + +  + I + N+PF  +  E+++ FS FGE+ +  +P     T   +G GF+ F
Sbjct: 6   SGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDF 65

Query: 475 KTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
            T + A  A +A          L GR+L +  A  + 
Sbjct: 66  ITKQDAKKAFNALCH----STHLYGRRLVLEWADSEV 98

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 4   KKGSNEHRGFGYVQFAVMEDANRAVE-MKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
             G+  HRGFG+V F   +DA +A   + + T + GR++ ++ A    +++   S 
Sbjct: 51  MTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106

>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 Length = 111

 Score = 92.8 bits (231), Expect = 7e-23
 Identities = 40/112 (35%), Positives = 53/112 (47%), Gaps = 6/112 (5%)

Query: 407 SSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRP 466
           SS S       TEG      T+FI NL FD + E + +    FG++     VLH  T+  
Sbjct: 2   SSGSSGLPSDVTEG-----KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHS 56

Query: 467 KGTGFLKFKTVEAATAAVSA-SKTTSGLGIFLKGRQLTVLKALDKKLAHDKE 517
           KG  F +F T EAA   ++A S    G G+ L GRQL V  A+ +  A    
Sbjct: 57  KGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGP 108

>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 Length = 111

 Score = 80.9 bits (200), Expect = 1e-18
 Identities = 24/94 (25%), Positives = 45/94 (47%), Gaps = 6/94 (6%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            + IRN+ F ++   + ++    G +  V +  + DT  SKG AF +F  +  A+  +  
Sbjct: 17  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76

Query: 278 FN------GQKFGKRPIAVDWAVPKNIYSSGGAA 305
            +      G K   R + VD AV ++  +SG ++
Sbjct: 77  ASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSS 110

>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 Length = 111

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 6/63 (9%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKN------GTSVGGRKIGVKHAMHRASLEQ 54
           +V    +   +G  + QF   E A + +   +      G  + GR++ V  A+ R     
Sbjct: 47  VVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106

Query: 55  RRS 57
             S
Sbjct: 107 GPS 109

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 90.4 bits (225), Expect = 5e-22
 Identities = 23/80 (28%), Positives = 45/80 (56%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           W L +  +  +A   +I D F+  G + N+++  +  TG  KG+  V++   ++A++A++
Sbjct: 24  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 277 KFNGQKFGKRPIAVDWAVPK 296
             NGQ    +PI+VDW   +
Sbjct: 84  GLNGQDLMGQPISVDWCFVR 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 72.7 bits (179), Expect = 8e-16
 Identities = 21/112 (18%), Positives = 46/112 (41%), Gaps = 10/112 (8%)

Query: 400 SDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVL 459
            D   +     +P   +  EG       +F+  +  +   E++  +F+ +GE+ +    L
Sbjct: 3   EDYDSVEQDGDEPGPQRSVEG-----WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL 57

Query: 460 HQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
            + T   KG   ++++T + A AA+         G  L G+ ++V     + 
Sbjct: 58  DRRTGYLKGYTLVEYETYKEAQAAMEGLN-----GQDLMGQPISVDWCFVRG 104

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 46.9 bits (112), Expect = 8e-07
 Identities = 11/50 (22%), Positives = 23/50 (46%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRA 50
           +   + +   +G+  V++   ++A  A+E  NG  + G+ I V     R 
Sbjct: 55  LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG 104

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 90.0 bits (224), Expect = 5e-22
 Identities = 24/90 (26%), Positives = 43/90 (47%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G          + + N+    +  +++++F P G +  +Y+  +  TG SKGFAF+ F  
Sbjct: 7   GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR 66

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKN 297
           + DA  AI   +G  +    + V+WA P  
Sbjct: 67  REDAARAIAGVSGFGYDHLILNVEWAKPST 96

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.6 bits (153), Expect = 2e-12
 Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 7/83 (8%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
            TI + NL  D    ++++ F  FG +        + T + KG  F+ F   E A  A++
Sbjct: 16  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75

Query: 486 ASKTTSGL-GIFLKGRQLTVLKA 507
                  + G       L V  A
Sbjct: 76  G------VSGFGYDHLILNVEWA 92

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 12/45 (26%), Positives = 21/45 (46%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
             K + + +GF ++ F   EDA RA+   +G       + V+ A
Sbjct: 48 AKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA 92

>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* Length = 110

 Score = 90.0 bits (224), Expect = 6e-22
 Identities = 25/80 (31%), Positives = 45/80 (56%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           W L + +I  +A+ +EI++ F   G + N+++  +  TG SKG+A V++   + A +A +
Sbjct: 27  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 86

Query: 277 KFNGQKFGKRPIAVDWAVPK 296
             NG +   + I VDW   K
Sbjct: 87  ALNGAEIMGQTIQVDWCFVK 106

>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* Length = 110

 Score = 68.9 bits (169), Expect = 2e-14
 Identities = 21/108 (19%), Positives = 47/108 (43%), Gaps = 10/108 (9%)

Query: 404 KLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVT 463
             +  + +P   +  EG       +F+ ++  +   +E++++F  +GE+ +    L + T
Sbjct: 10  NEDDDELEPGPQRSVEG-----WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRT 64

Query: 464 KRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
              KG   ++++T + A AA  A       G  + G+ + V     K 
Sbjct: 65  GFSKGYALVEYETHKQALAAKEALN-----GAEIMGQTIQVDWCFVKG 107

>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* Length = 110

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 10/39 (25%), Positives = 18/39 (46%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
           +G+  V++   + A  A E  NG  + G+ I V     +
Sbjct: 68  KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 106

>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 Length = 175

 Score = 91.9 bits (229), Expect = 8e-22
 Identities = 43/181 (23%), Positives = 77/181 (42%), Gaps = 17/181 (9%)

Query: 121 ARTVIIGGLLNADMAEE-VHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLY 179
           A  + +G +     +E+ +  L    G V  +   + ++  +    ++ GC      V +
Sbjct: 3   AIKMFVGQV-PRTWSEKDLRELFEQYGAVYEIN--VLRDRSQNPPQSK-GCCF----VTF 54

Query: 180 TTVKSACASVALLHQKEIKGGT---VWARQLGGEGSKTQKW-KLIIRNIPFKAKVNEIKD 235
            T K+A  +   LH  ++  G    +  +    E +   +  KL I  I  K   N+I+ 
Sbjct: 55  YTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRV 114

Query: 236 MFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF---GKRPIAVDW 292
           MFS  G +    I      GLS+G AFV FT +  A++AI+  +  +       P+ V +
Sbjct: 115 MFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKF 173

Query: 293 A 293
           A
Sbjct: 174 A 174

>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 Length = 175

 Score = 66.5 bits (163), Expect = 6e-13
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 4/86 (4%)

Query: 404 KLNSSKSKPKSLKQTEGEDELQNT---IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLH 460
           K+      P  +K  + E         +FI  +       +++  FS+FG++     +L 
Sbjct: 71  KVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE-CRILR 129

Query: 461 QVTKRPKGTGFLKFKTVEAATAAVSA 486
                 +G  F+ F T   A  A+ A
Sbjct: 130 GPDGLSRGCAFVTFTTRAMAQTAIKA 155

>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 Length = 175

 Score = 64.9 bits (159), Expect = 2e-12
 Identities = 37/238 (15%), Positives = 67/238 (28%), Gaps = 92/238 (38%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRP--KGTGFLKFKTVEAATAAV 484
            +F+  +P     +++++ F  +G V     +  +    P  KG  F+ F T +AA  A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 485 SASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTP 544
           +A          L   ++        ++   K  D  KN   + R L+            
Sbjct: 65  NA----------LHNMKVLPGMHHPIQM---KPADSEKNNAVEDRKLF------------ 99

Query: 545 AAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKL------C 598
                                                I  + K  TE  ++ +       
Sbjct: 100 -------------------------------------IGMISKKCTENDIRVMFSSFGQI 122

Query: 599 IDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN 656
            +  + R                           SRG AFV FT    A  A++ ++ 
Sbjct: 123 EECRILRGPDGL----------------------SRGCAFVTFTTRAMAQTAIKAMHQ 158

>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 Length = 175

 Score = 64.2 bits (157), Expect = 4e-12
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 2/82 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGL--SKGFAFVKFTCKRDAESAI 275
           K+ +  +P      +++++F   G V+ + +  +       SKG  FV F  ++ A  A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 276 QKFNGQKFGKRPIAVDWAVPKN 297
              +  K            P +
Sbjct: 65  NALHNMKVLPGMHHPIQMKPAD 86

>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 Length = 175

 Score = 43.8 bits (104), Expect = 4e-05
 Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 13/80 (16%)

Query: 577 RTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGV 636
             ++ +  +P++ +EK L++L       +       + +I     + + +      S+G 
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELF-----EQYGA----VYEIN----VLRDRSQNPPQSKGC 49

Query: 637 AFVEFTEHQHALVALRVLNN 656
            FV F   + AL A   L+N
Sbjct: 50  CFVTFYTRKAALEAQNALHN 69

>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 Length = 175

 Score = 40.7 bits (96), Expect = 4e-04
 Identities = 11/71 (15%), Positives = 21/71 (29%), Gaps = 1/71 (1%)

Query: 6   GSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQA 65
              + +G  +V F   + A  A    +   V             A  E+  +   +++  
Sbjct: 42  NPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQM-KPADSEKNNAVEDRKLFI 100

Query: 66  EDIEKTMDNKD 76
             I K     D
Sbjct: 101 GMISKKCTEND 111

>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 Length = 99

 Score = 89.6 bits (223), Expect = 9e-22
 Identities = 27/99 (27%), Positives = 48/99 (48%)

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
           G    +   +L +RN+ + +   +++ +FS  G +  ++ P ++ T   KGFAFV F   
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 269 RDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAG 307
             A  A  + +GQ F  R + V  +  K   S  G ++G
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>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 Length = 99

 Score = 72.6 bits (179), Expect = 6e-16
 Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 7/87 (8%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             +F+ NL +    E++++ FSA+G +      +  +TK+PKG  F+ F   E A  A +
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 486 ASKTTSGL-GIFLKGRQLTVLKALDKK 511
                  + G   +GR L VL +  KK
Sbjct: 69  E------VDGQVFQGRMLHVLPSTIKK 89

>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 Length = 99

 Score = 49.1 bits (118), Expect = 1e-07
 Identities = 12/58 (20%), Positives = 21/58 (36%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
                + + +GF +V F   E A +A    +G    GR + V  +  +    Q    
Sbjct: 40 YPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPS 97

>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* Length = 126

 Score = 89.7 bits (223), Expect = 1e-21
 Identities = 23/99 (23%), Positives = 48/99 (48%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           W L +  +  +A   +I D F+  G + N+++  +  TG  KG+  V++   ++A++A++
Sbjct: 23  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 277 KFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGN 315
             NGQ    +PI+VDW   +            +++    
Sbjct: 83  GLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPDR 121

>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* Length = 126

 Score = 72.0 bits (177), Expect = 2e-15
 Identities = 21/112 (18%), Positives = 46/112 (41%), Gaps = 10/112 (8%)

Query: 400 SDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVL 459
            D   +     +P   +  EG       +F+  +  +   E++  +F+ +GE+ +    L
Sbjct: 2   EDYDSVEQDGDEPGPQRSVEG-----WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL 56

Query: 460 HQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
            + T   KG   ++++T + A AA+         G  L G+ ++V     + 
Sbjct: 57  DRRTGYLKGYTLVEYETYKEAQAAMEGLN-----GQDLMGQPISVDWCFVRG 103

>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* Length = 126

 Score = 48.1 bits (115), Expect = 5e-07
 Identities = 12/58 (20%), Positives = 26/58 (44%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
           +   + +   +G+  V++   ++A  A+E  NG  + G+ I V     R   + +R  
Sbjct: 54  LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRG 111

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 87.3 bits (217), Expect = 5e-21
 Identities = 26/88 (29%), Positives = 44/88 (50%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L + N+ ++   + ++ +F   G V +VYIP    T   +GFAFV+F  +RDA+ A   
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGGAA 305
            +G +   R + V  A       SG ++
Sbjct: 75  MDGAELDGRELRVQVARYGRRDLSGPSS 102

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 67.3 bits (165), Expect = 5e-14
 Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 7/89 (7%)

Query: 420 GEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
            + +   T+ + NL +    + +++ F  +G V          TK P+G  F++F     
Sbjct: 8   PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67

Query: 480 ATAAVSASKTTSGL-GIFLKGRQLTVLKA 507
           A  A +A      + G  L GR+L V  A
Sbjct: 68  AQDAEAA------MDGAELDGRELRVQVA 90

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 51.1 bits (123), Expect = 3e-08
 Identities = 13/49 (26%), Positives = 24/49 (48%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
          +  +  +   RGF +V+F    DA  A    +G  + GR++ V+ A + 
Sbjct: 45 IPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYG 93

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 87.5 bits (217), Expect = 1e-20
 Identities = 28/99 (28%), Positives = 44/99 (44%)

Query: 198 KGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLS 257
           + G                  L + N+ ++   + ++ +F   G V +VYIP +  T  S
Sbjct: 29  QMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKES 88

Query: 258 KGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           +GFAFV+F  KRDAE A+   +G     R + V  A   
Sbjct: 89  RGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 127

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 68.2 bits (167), Expect = 6e-14
 Identities = 22/103 (21%), Positives = 40/103 (38%), Gaps = 7/103 (6%)

Query: 406 NSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKR 465
                   S  +   + E   ++ + NL +    + +++ F  +G V        + TK 
Sbjct: 28  QQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE 87

Query: 466 PKGTGFLKFKTVEAATAAVSASKTTSGL-GIFLKGRQLTVLKA 507
            +G  F++F     A  A+ A      + G  L GR+L V  A
Sbjct: 88  SRGFAFVRFHDKRDAEDAMDA------MDGAVLDGRELRVQMA 124

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 51.7 bits (124), Expect = 4e-08
 Identities = 15/51 (29%), Positives = 27/51 (52%)

Query: 7   SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           + E RGF +V+F    DA  A++  +G  + GR++ V+ A +    +   S
Sbjct: 85  TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHHS 135

>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 Length = 98

 Score = 86.2 bits (214), Expect = 1e-20
 Identities = 19/89 (21%), Positives = 36/89 (40%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G    K     + ++N+PF   ++EI D F    ++         + G+  G A V F  
Sbjct: 7   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           + +A +A+   N +  G R + +      
Sbjct: 67  RDEATAAVIDLNDRPIGSRKVKLVLGSGP 95

>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 Length = 98

 Score = 58.5 bits (142), Expect = 7e-11
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             I + N+PF +  +E+   F  +  +   V + +     P G   + F++ + ATAAV 
Sbjct: 16  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 486 ASKTTSGLGIFLKGRQLTVLKA 507
                      +  R++ ++  
Sbjct: 76  DLN-----DRPIGSRKVKLVLG 92

>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 Length = 98

 Score = 47.3 bits (113), Expect = 6e-07
 Identities = 10/36 (27%), Positives = 15/36 (41%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           G   V F   ++A  AV   N   +G RK+ +   
Sbjct: 57 TGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 92

>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 Length = 95

 Score = 85.8 bits (213), Expect = 1e-20
 Identities = 19/86 (22%), Positives = 36/86 (41%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G    K     + ++N+PF   ++EI D F    ++         + G+  G A V F  
Sbjct: 7   GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWA 293
           + +A +A+   N +  G R + +   
Sbjct: 67  RDEATAAVIDLNDRPIGSRKVKLSGP 92

>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 Length = 95

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 16/91 (17%), Positives = 34/91 (37%), Gaps = 5/91 (5%)

Query: 417 QTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKT 476
            +         I + N+PF +  +E+   F  +  +   V + +     P G   + F++
Sbjct: 7   GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66

Query: 477 VEAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
            + ATAAV            +  R++ +   
Sbjct: 67  RDEATAAVIDLN-----DRPIGSRKVKLSGP 92

>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 Length = 95

 Score = 46.9 bits (112), Expect = 8e-07
 Identities = 10/33 (30%), Positives = 15/33 (45%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
           G   V F   ++A  AV   N   +G RK+ +
Sbjct: 57 TGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL 89

>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 Length = 165

 Score = 87.6 bits (217), Expect = 2e-20
 Identities = 25/82 (30%), Positives = 46/82 (56%)

Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           + W L + +I  +A+ +EI++ F   G + N+++  +  TG SKG+A V++   + A +A
Sbjct: 71  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130

Query: 275 IQKFNGQKFGKRPIAVDWAVPK 296
            +  NG +   + I VDW   K
Sbjct: 131 KEALNGAEIMGQTIQVDWCFVK 152

>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 Length = 165

 Score = 72.9 bits (179), Expect = 3e-15
 Identities = 29/169 (17%), Positives = 64/169 (37%), Gaps = 21/169 (12%)

Query: 343 DLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDV 402
           D+ +  +F+ + D  +            +  L + +   KG        T         V
Sbjct: 6   DIDNAEEFEVDEDGDQ-----------GIVRLKEKAKHRKGRGFGSDSNTREAIHSYERV 54

Query: 403 SKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQV 462
              +  + +P   +  EG       +F+ ++  +   +E++++F  +GE+ +    L + 
Sbjct: 55  RNEDDDELEPGPQRSVEG-----WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR 109

Query: 463 TKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           T   KG   ++++T + A AA  A       G  + G+ + V     K 
Sbjct: 110 TGFSKGYALVEYETHKQALAAKEALN-----GAEIMGQTIQVDWCFVKG 153

>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 Length = 165

 Score = 50.6 bits (121), Expect = 2e-07
 Identities = 11/58 (18%), Positives = 25/58 (43%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
           +   + +   +G+  V++   + A  A E  NG  + G+ I V     +     ++S+
Sbjct: 104 LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSE 161

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 85.0 bits (211), Expect = 3e-20
 Identities = 30/96 (31%), Positives = 44/96 (45%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G  G  T K  L +  +  +     +   F P G + ++ IP + +T   +GFAFV+F  
Sbjct: 4   GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 63

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGG 303
             DA +AI   N  +   R I V+ A P  I  SG 
Sbjct: 64  AEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESGP 99

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 63.4 bits (155), Expect = 1e-12
 Identities = 20/94 (21%), Positives = 41/94 (43%), Gaps = 5/94 (5%)

Query: 418 TEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTV 477
           + G    +  +++  L  ++D++ +   F  FG++      L   T++ +G  F++F+  
Sbjct: 5   SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 64

Query: 478 EAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           E A AA+            L GR + V  A   +
Sbjct: 65  EDAAAAIDNMN-----ESELFGRTIRVNLAKPMR 93

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 50.3 bits (121), Expect = 4e-08
 Identities = 18/57 (31%), Positives = 28/57 (49%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           +     + +HRGF +V+F + EDA  A++  N + + GR I V  A      E   S
Sbjct: 44  IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESGPS 100

>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: 3h2u_B 3h2v_E Length = 284

 Score = 90.4 bits (225), Expect = 4e-20
 Identities = 28/145 (19%), Positives = 56/145 (38%), Gaps = 12/145 (8%)

Query: 157 KEELEQHGLAQEGCKMDASA----VLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGS 212
            + L  + L  + C +D       V     + A A++   HQ  ++   +  +       
Sbjct: 40  HDLLSDYEL--KYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL------ 91

Query: 213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAE 272
           +     L + N+P      + +++  P G +   ++ ++  TG SKG+ F ++  K  A 
Sbjct: 92  QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAA 151

Query: 273 SAIQKFNGQKFGKRPIAVDWAVPKN 297
            A     G+  G R + V W     
Sbjct: 152 RAKSDLLGKPLGPRTLYVHWTDAGQ 176

>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: 3h2u_B 3h2v_E Length = 284

 Score = 77.3 bits (191), Expect = 9e-16
 Identities = 24/125 (19%), Positives = 41/125 (32%), Gaps = 5/125 (4%)

Query: 177 VLYTTVKSACASVALLHQKEIKGGTV---WARQLGGEGSKTQKWKLIIRNIPFKAKVNE- 232
             Y    SA  + + L  K +   T+   W        +      L +  +P      + 
Sbjct: 142 AEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDA 201

Query: 233 IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW 292
           +    S V       +      G  KGFA +++     AE A Q+ +G   G   + V +
Sbjct: 202 LCRALSAVHSPTFCQLACG-QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260

Query: 293 AVPKN 297
             P  
Sbjct: 261 CAPGP 265

>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: 3h2u_B 3h2v_E Length = 284

 Score = 73.9 bits (182), Expect = 1e-14
 Identities = 24/110 (21%), Positives = 40/110 (36%), Gaps = 13/110 (11%)

Query: 191 LLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPH 250
           +L  +EI+           E     + K++IR +P      E+ D+ S   L        
Sbjct: 2   MLDPEEIR--KRLEHT---ERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELK------- 49

Query: 251 NTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK-NIY 299
                  KG AFV       AE+AI  F+  +  +R ++V        + 
Sbjct: 50  YCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLC 99

>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: 3h2u_B 3h2v_E Length = 284

 Score = 69.6 bits (171), Expect = 4e-13
 Identities = 44/283 (15%), Positives = 77/283 (27%), Gaps = 75/283 (26%)

Query: 409 KSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKG 468
           +   K L+ TE +   +  I I  LP D+ N+EV    S +        + +    + KG
Sbjct: 6   EEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKG 58

Query: 469 TGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA--------------------- 507
           T F+     E A AA++A          L+ R+L+V                        
Sbjct: 59  TAFVTLLNGEQAEAAINAFH-----QSRLRERELSVQLQPTDALLCVANLPPSLTQQQFE 113

Query: 508 ---------LDKKLAHDKEIDKSKN----ETNDHRNLYLAKEGLILEGTPAAEGVSDDDM 554
                        L + +   +SK     E     +   AK  L                
Sbjct: 114 ELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL------------LGKP 161

Query: 555 SKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTE-KGLKKLCIDAVVSRASKQKPVI 613
              + L+       Q     +    L +  LP    +   L +                 
Sbjct: 162 LGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRAL---------SAVHSP 212

Query: 614 KQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN 656
              +                +G A +E+   + A  A +  + 
Sbjct: 213 TFCQLAC-------GQDGQLKGFAVLEYETAEMAEEAQQQADG 248

>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: 3h2u_B 3h2v_E Length = 284

 Score = 69.2 bits (170), Expect = 4e-13
 Identities = 25/122 (20%), Positives = 47/122 (38%), Gaps = 9/122 (7%)

Query: 402 VSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQ 461
           ++  + S+ + + L       +    + + NLP  L  ++ ++    FG +     V  +
Sbjct: 74  INAFHQSRLRERELSVQLQPTD--ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSE 131

Query: 462 VTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKS 521
            T + KG GF ++   ++A  A S       LG  L  R L V    D        +  S
Sbjct: 132 RTGQSKGYGFAEYMKKDSAARAKSDL-----LGKPLGPRTLYVHWT-DAGQLTPALL-HS 184

Query: 522 KN 523
           + 
Sbjct: 185 RC 186

>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: 3h2u_B 3h2v_E Length = 284

 Score = 60.4 bits (147), Expect = 3e-10
 Identities = 22/117 (18%), Positives = 36/117 (30%), Gaps = 14/117 (11%)

Query: 402 VSKLNSSKSKPKSL-------KQTEGEDELQNTIFICNLPFDL-DNEEVKQRFSAFGEVV 453
            S L      P++L        Q          + +  LP    D + + +  SA     
Sbjct: 154 KSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPT 213

Query: 454 SFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
               +      + KG   L+++T E A  A   +      G+ L G  L V      
Sbjct: 214 F-CQLACGQDGQLKGFAVLEYETAEMAEEAQQQAD-----GLSLGGSHLRVSFCAPG 264

>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: 3h2u_B 3h2v_E Length = 284

 Score = 51.5 bits (124), Expect = 3e-07
 Identities = 10/46 (21%), Positives = 22/46 (47%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           +V  + + + +G+G+ ++   + A RA     G  +G R + V   
Sbjct: 127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT 172

>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: 3h2u_B 3h2v_E Length = 284

 Score = 48.1 bits (115), Expect = 4e-06
 Identities = 9/45 (20%), Positives = 21/45 (46%)

Query: 8  NEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASL 52
          ++++G  +V     E A  A+   + + +  R++ V+     A L
Sbjct: 54 DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALL 98

>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: 3h2u_B 3h2v_E Length = 284

 Score = 47.7 bits (114), Expect = 5e-06
 Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 3/64 (4%)

Query: 2   VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQ 61
           +      + +GF  +++   E A  A +  +G S+GG  + V            RS +  
Sbjct: 217 LACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG---PPGRSMLAA 273

Query: 62  EVQA 65
            + A
Sbjct: 274 LIAA 277

>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 Length = 282

 Score = 89.9 bits (222), Expect = 4e-20
 Identities = 37/272 (13%), Positives = 78/272 (28%), Gaps = 24/272 (8%)

Query: 219 LIIRNIPFKAKVNEIK----DMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           + I N+  K K +E+K     +FS  G + ++ +     +   +G AFV F     A +A
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 68

Query: 275 IQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASD 334
           ++   G  F  +P+ + +A   +   +      V+             +           
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128

Query: 335 DSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVN 394
            +                     R + +         P        +   +         
Sbjct: 129 GATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQ 188

Query: 395 ESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS 454
           +            S++ P             + +F+ NLP + +   +   F+ F     
Sbjct: 189 QLMPGQMPPAQPLSENPP------------NHILFLTNLPEETNELMLSMLFNQFPGFKE 236

Query: 455 FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
                 ++        F++F     A AA  A
Sbjct: 237 -----VRLVPGRHDIAFVEFDNEVQAGAARDA 263

>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 Length = 282

 Score = 68.7 bits (167), Expect = 7e-13
 Identities = 43/267 (16%), Positives = 74/267 (27%), Gaps = 46/267 (17%)

Query: 426 NTIFICNLPFDLDNEEVKQR----FSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAAT 481
           +TI+I NL   +  +E+K+     FS FG+++  + V    + + +G  F+ FK V +AT
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDIL-VSR--SLKMRGQAFVIFKEVSSAT 66

Query: 482 AAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLIL- 540
            A+ + +     G     + + +  A        K                   +     
Sbjct: 67  NALRSMQ-----GFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPAT 121

Query: 541 --------------EGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLP 586
                                G+     + R M H         P   +    L    +P
Sbjct: 122 KKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIP 181

Query: 587 KSMTEKGLKKLCIDAVVSRASKQKPVIKQIKF----------LQSL-------KKGKVDT 629
                               S+  P                 L  L       K+ ++  
Sbjct: 182 PGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP 241

Query: 630 KHYSRGVAFVEFTEHQHALVALRVLNN 656
                 +AFVEF     A  A   L  
Sbjct: 242 G--RHDIAFVEFDNEVQAGAARDALQG 266

>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 Length = 282

 Score = 47.9 bits (113), Expect = 5e-06
 Identities = 14/83 (16%), Positives = 28/83 (33%), Gaps = 6/83 (7%)

Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDA 271
                  L + N+P +     +  +F+       V +            AFV+F  +  A
Sbjct: 203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQA 257

Query: 272 ESAIQKFNGQKFGK-RPIAVDWA 293
            +A     G K  +   + + +A
Sbjct: 258 GAARDALQGFKITQNNAMKISFA 280

>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 Length = 282

 Score = 41.8 bits (97), Expect = 4e-04
 Identities = 9/55 (16%), Positives = 22/55 (40%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRR 56
          +    S + RG  +V F  +  A  A+    G     + + +++A   + +  + 
Sbjct: 43 ILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 97

>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 Length = 282

 Score = 41.4 bits (96), Expect = 6e-04
 Identities = 24/77 (31%), Positives = 29/77 (37%), Gaps = 14/77 (18%)

Query: 582 IYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEF 641
           I NL + + +  LKK            Q   I  I   +SLK          RG AFV F
Sbjct: 14  INNLNEKIKKDELKKSLYAI-----FSQFGQILDILVSRSLK---------MRGQAFVIF 59

Query: 642 TEHQHALVALRVLNNNP 658
            E   A  ALR +   P
Sbjct: 60  KEVSSATNALRSMQGFP 76

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 83.4 bits (207), Expect = 1e-19
 Identities = 23/75 (30%), Positives = 41/75 (54%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           +IP+     +I D+ S VG V N+ +  +  TG SKG+AF++F     + SA++  NG +
Sbjct: 9   SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 68

Query: 283 FGKRPIAVDWAVPKN 297
            G R +   ++   +
Sbjct: 69  LGSRFLKCGYSSNSD 83

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 73.0 bits (180), Expect = 5e-16
 Identities = 21/105 (20%), Positives = 44/105 (41%), Gaps = 14/105 (13%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            +++ ++P+D   E++    S  G V++   +    T R KG  F++F+ +E++ +AV  
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 487 SKTTSGL-GIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRN 530
                 L G  L  R L    + +             +  + H +
Sbjct: 64  ------LNGYQLGSRFLKCGYSSNSD-------ISGVSLEHHHHH 95

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 52.6 bits (127), Expect = 8e-09
 Identities = 10/57 (17%), Positives = 24/57 (42%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          M+    +   +G+ +++F  +E +  AV   NG  +G R +   ++ +         
Sbjct: 34 MMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDISGVSLE 90

>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 Length = 156

 Score = 84.9 bits (210), Expect = 2e-19
 Identities = 26/105 (24%), Positives = 49/105 (46%), Gaps = 3/105 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L + N+ F     +I ++FS  G +  + +  +     + GF FV++  + DAE+A++ 
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100

Query: 278 FNGQKFGKRPIAVDWAVPK---NIYSSGGAAAGVQNKGDGNSDSG 319
            NG +   R I  DW         Y  G +   V+++   + D+G
Sbjct: 101 INGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAG 145

>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 Length = 156

 Score = 68.3 bits (167), Expect = 9e-14
 Identities = 24/117 (20%), Positives = 44/117 (37%), Gaps = 15/117 (12%)

Query: 405 LNSSKSKPKSL---KQTEGEDELQ-------NTIFICNLPFDLDNEEVKQRFSAFGEVVS 454
           L S      S    +   G++E Q        T+++ NL F    E++ + FS  G++  
Sbjct: 9   LRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKK 68

Query: 455 FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
            +  L ++ K   G  F+++ +   A  A+         G  L  R +        K
Sbjct: 69  IIMGLDKMKKTACGFCFVEYYSRADAENAMRYIN-----GTRLDDRIIRTDWDAGFK 120

>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 Length = 156

 Score = 49.4 bits (118), Expect = 4e-07
 Identities = 14/54 (25%), Positives = 19/54 (35%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQ 54
           M   K      GF +V++    DA  A+   NGT +  R I            Q
Sbjct: 71  MGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQ 124

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-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 Length = 168

 Score = 84.2 bits (209), Expect = 3e-19
 Identities = 35/178 (19%), Positives = 74/178 (41%), Gaps = 19/178 (10%)

Query: 122 RTVIIGGLLNADMAEE-VHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYT 180
             +I+  L   DM +  ++ L  +IG + +       +    +G A          V +T
Sbjct: 4   TNLIVNYL-PQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYA---------FVDFT 53

Query: 181 TVKSACASVALLHQKEIKGGTV---WARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMF 237
           +   +  ++ +L+   ++   +   +AR     G   +   L + N+P     +++  +F
Sbjct: 54  SEMDSQRAIKVLNGITVRNKRLKVSYARP---GGESIKDTNLYVTNLPRTITDDQLDTIF 110

Query: 238 SPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF--GKRPIAVDWA 293
              G +    I  +  TG  +G AFV++  + +A+ AI   N      G +P++V  A
Sbjct: 111 GKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-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 Length = 168

 Score = 80.7 bits (200), Expect = 6e-18
 Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 7/89 (7%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            LI+  +P      E+  +F  +G +    I  +  TG S G+AFV FT + D++ AI+ 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 278 FNGQKFGKRPIAVDWAVPK-------NIY 299
            NG     + + V +A P        N+Y
Sbjct: 65  LNGITVRNKRLKVSYARPGGESIKDTNLY 93

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-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 Length = 168

 Score = 74.9 bits (185), Expect = 7e-16
 Identities = 41/230 (17%), Positives = 72/230 (31%), Gaps = 81/230 (35%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            + +  LP D+ + E+   F A G + +   +    T    G  F+ F +   +  A+  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 487 SKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAA 546
                  GI ++ ++L V  A            +   E+    NLY              
Sbjct: 65  LN-----GITVRNKRLKVSYA------------RPGGESIKDTNLY-------------- 93

Query: 547 EGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRA 606
                                              + NLP+++T+  L  +         
Sbjct: 94  -----------------------------------VTNLPRTITDDQLDTIF-------- 110

Query: 607 SKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN 656
             +   I Q   L+    G+       RGVAFV + + + A  A+  LNN
Sbjct: 111 -GKYGSIVQKNILRDKLTGR------PRGVAFVRYNKREEAQEAISALNN 153

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-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 Length = 168

 Score = 68.4 bits (168), Expect = 1e-13
 Identities = 23/89 (25%), Positives = 44/89 (49%), Gaps = 4/89 (4%)

Query: 402 VSKLNSSKSKPKSLK----QTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVP 457
           +  LN    + K LK    +  GE      +++ NLP  + ++++   F  +G +V    
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121

Query: 458 VLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           +  ++T RP+G  F+++   E A  A+SA
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISA 150

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-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 Length = 168

 Score = 51.4 bits (124), Expect = 1e-07
 Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 4/60 (6%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
          ++    +    G+ +V F    D+ RA+++ NG +V  +++ V      A       K T
Sbjct: 35 IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVS----YARPGGESIKDT 90

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-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 Length = 168

 Score = 40.2 bits (95), Expect = 5e-04
 Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 19/83 (22%)

Query: 576 SRTRLVIYNLPKSMTEKGLKKLCIDA--VVSRASKQKPVIKQIKFLQSLKKGKVDTKHYS 633
           S T L++  LP+ MT++ L  L      + +         + ++  ++          YS
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINT--------CRIMRDYKT---------GYS 44

Query: 634 RGVAFVEFTEHQHALVALRVLNN 656
            G AFV+FT    +  A++VLN 
Sbjct: 45  YGYAFVDFTSEMDSQRAIKVLNG 67

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 81.9 bits (203), Expect = 3e-19
 Identities = 27/94 (28%), Positives = 41/94 (43%), Gaps = 7/94 (7%)

Query: 208 GGEGSKTQKW-------KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGF 260
           G  GS             + + N+PF    N++  +FS  G V  V I  + DT  SKG 
Sbjct: 1   GSSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGV 60

Query: 261 AFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV 294
           AF+ F  K  A++  +  N ++   R I    A+
Sbjct: 61  AFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI 94

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 72.6 bits (179), Expect = 7e-16
 Identities = 25/96 (26%), Positives = 46/96 (47%), Gaps = 7/96 (7%)

Query: 414 SLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLK 473
           S   + G    ++T+++ NLPF L N ++ + FS +G+VV    +  + T++ KG  F+ 
Sbjct: 5   SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFIL 64

Query: 474 FKTVEAATAAVSASKTTSGL-GIFLKGRQLTVLKAL 508
           F   ++A     A      +    L GR +    A+
Sbjct: 65  FLDKDSAQNCTRA------INNKQLFGRVIKASIAI 94

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 9/47 (19%), Positives = 19/47 (40%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAM 47
          ++  K + + +G  ++ F   + A       N   + GR I    A+
Sbjct: 48 IMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI 94

>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 Length = 104

 Score = 81.9 bits (203), Expect = 4e-19
 Identities = 26/74 (35%), Positives = 46/74 (62%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           NIP++A   ++KD+FS VG V +  + ++ +TG  KG+ F ++  +  A SA++  NG++
Sbjct: 15  NIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGRE 74

Query: 283 FGKRPIAVDWAVPK 296
           F  R + VD A  +
Sbjct: 75  FSGRALRVDNAASE 88

>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 Length = 104

 Score = 71.5 bits (176), Expect = 2e-15
 Identities = 31/91 (34%), Positives = 47/91 (51%), Gaps = 7/91 (7%)

Query: 422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAAT 481
           D    ++F+ N+P++   E++K  FS  G VVSF  V  + T +PKG GF +++  E A 
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 482 AAVSASKTTSGL-GIFLKGRQLTVLKALDKK 511
           +A+        L G    GR L V  A  +K
Sbjct: 65  SAMRN------LNGREFSGRALRVDNAASEK 89

>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 Length = 104

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 14/57 (24%), Positives = 29/57 (50%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          +V  + + + +G+G+ ++   E A  A+   NG    GR + V +A    + E+ +S
Sbjct: 40 LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKS 96

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 83.7 bits (207), Expect = 4e-19
 Identities = 27/93 (29%), Positives = 43/93 (46%)

Query: 204 ARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFV 263
           +              L + N+ ++   + ++ +F   G V +VYIP +  T  S+GFAFV
Sbjct: 58  SHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 117

Query: 264 KFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           +F  KRDAE A+   +G     R + V  A   
Sbjct: 118 RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 150

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 70.3 bits (172), Expect = 2e-14
 Identities = 27/153 (17%), Positives = 59/153 (38%), Gaps = 5/153 (3%)

Query: 359 KVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQT 418
           K++    +  G   + + D+A  +   +Q ++    +     D +    + ++       
Sbjct: 4   KLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHH 63

Query: 419 EGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVE 478
             + E   ++ + NL +    + +++ F  +G V        + TK  +G  F++F    
Sbjct: 64  HMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR 123

Query: 479 AATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
            A  A+ A       G  L GR+L V  A   +
Sbjct: 124 DAEDAMDAMD-----GAVLDGRELRVQMARYGR 151

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 53.3 bits (128), Expect = 2e-08
 Identities = 15/57 (26%), Positives = 29/57 (50%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           +   + + E RGF +V+F    DA  A++  +G  + GR++ V+ A +    +   S
Sbjct: 102 IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHHS 158

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 83.3 bits (206), Expect = 4e-19
 Identities = 24/93 (25%), Positives = 40/93 (43%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L++  IP      +++ +F   G + +V I  + +T  S+G+ FVKF     A+ AI  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQN 310
            NG     + + V  A   +       A G  N
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIAGAVGDGN 136

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 72.9 bits (179), Expect = 1e-15
 Identities = 26/132 (19%), Positives = 54/132 (40%), Gaps = 13/132 (9%)

Query: 402 VSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQ 461
           + +L   + +     Q   E ++   + +  +P  +D  +++Q F  +G + S   V  +
Sbjct: 19  LQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR 78

Query: 462 VTKRPKGTGFLKFKTVEAATAAVSASKTTSGL-GIFLKGRQLTVLKALDKKLAHDKEIDK 520
            T++ +G GF+KF++  +A  A++       L G  +  ++L V       LA       
Sbjct: 79  ETRQSRGYGFVKFQSGSSAQQAIAG------LNGFNILNKRLKV------ALAASGHQRP 126

Query: 521 SKNETNDHRNLY 532
                    N Y
Sbjct: 127 GIAGAVGDGNGY 138

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 45.5 bits (108), Expect = 6e-06
 Identities = 11/36 (30%), Positives = 21/36 (58%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           RG+G+V+F     A +A+   NG ++  +++ V  A
Sbjct: 84  RGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA 119

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 81.4 bits (202), Expect = 5e-19
 Identities = 23/88 (26%), Positives = 46/88 (52%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L + ++ F    + ++ +F P G + N+ +  ++DTG SKG+ F+ F+    A  A+++
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGGAA 305
            NG +   RP+ V     +    SG ++
Sbjct: 67  LNGFELAGRPMRVGHVTERLDGGSGPSS 94

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 67.6 bits (166), Expect = 4e-14
 Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 7/86 (8%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           + +++ +L F++  + ++  F  FG++ + V +    T R KG GF+ F   E A  A+ 
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 486 ASKTTSGL-GIFLKGRQLTVLKALDK 510
                  L G  L GR + V    ++
Sbjct: 66  Q------LNGFELAGRPMRVGHVTER 85

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 49.5 bits (119), Expect = 7e-08
 Identities = 16/57 (28%), Positives = 27/57 (47%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          ++    +   +G+G++ F+  E A RA+E  NG  + GR + V H   R       S
Sbjct: 37 LMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDGGSGPS 93

>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 Length = 105

 Score = 81.6 bits (202), Expect = 7e-19
 Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 4/93 (4%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G E    +  KL +  +  +    ++  +F P G++    +      G SKG AFVKF+ 
Sbjct: 7   GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSS 65

Query: 268 KRDAESAIQKFNGQKF---GKRPIAVDWAVPKN 297
             +A++AI   +G +        + V +A    
Sbjct: 66  HTEAQAAIHALHGSQTMPGASSSLVVKFADTDK 98

>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 Length = 105

 Score = 61.5 bits (150), Expect = 6e-12
 Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 410 SKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGT 469
           S   S  ++ G  +    +F+  L      E+V + F  FG +     VL       KG 
Sbjct: 2   SSGSSGSESRGGRD--RKLFVGMLNKQQSEEDVLRLFQPFGVIDE-CTVLRGPDGSSKGC 58

Query: 470 GFLKFKTVEAATAAVSA 486
            F+KF +   A AA+ A
Sbjct: 59  AFVKFSSHTEAQAAIHA 75

>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 Length = 105

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 20/81 (24%)

Query: 578 TRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKP--VIKQIKFLQSLKKGKVDTKHYSRG 635
            +L +  L K  +E+ + +L            +P  VI +   L+            S+G
Sbjct: 16  RKLFVGMLNKQQSEEDVLRLF-----------QPFGVIDECTVLR-------GPDGSSKG 57

Query: 636 VAFVEFTEHQHALVALRVLNN 656
            AFV+F+ H  A  A+  L+ 
Sbjct: 58  CAFVKFSSHTEAQAAIHALHG 78

>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 Length = 105

 Score = 38.8 bits (91), Expect = 7e-04
 Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 3/48 (6%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSV---GGRKIGVKHA 46
          V +      +G  +V+F+   +A  A+   +G+         + VK A
Sbjct: 47 VLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFA 94

>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 Length = 167

 Score = 83.0 bits (206), Expect = 8e-19
 Identities = 46/178 (25%), Positives = 79/178 (44%), Gaps = 21/178 (11%)

Query: 123 TVIIGGLLNADMAEE-VHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASA-VLYT 180
            +I+  L   +M +E    L GSIG + S    L ++++    L   G        V Y 
Sbjct: 4   NLIVNYL-PQNMTQEEFRSLFGSIGEIESCK--LVRDKITGQSL---GY-----GFVNYI 52

Query: 181 TVKSACASVALLHQKEIKGGTV---WARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMF 237
             K A  ++  L+   ++  T+   +AR      +  +   L +  +P      E++ +F
Sbjct: 53  DPKDAEKAINTLNGLRLQTKTIKVSYARP---SSASIRDANLYVSGLPKTMTQKELEQLF 109

Query: 238 SPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF--GKRPIAVDWA 293
           S  G +    I  +  TG+S+G  F++F  + +AE AI+  NGQK      PI V +A
Sbjct: 110 SQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>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 Length = 167

 Score = 76.8 bits (190), Expect = 1e-16
 Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 7/89 (7%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            LI+  +P      E + +F  +G + +  +  +  TG S G+ FV +   +DAE AI  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 278 FNGQKFGKRPIAVDWAVPK-------NIY 299
            NG +   + I V +A P        N+Y
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASIRDANLY 92

>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 Length = 167

 Score = 67.6 bits (166), Expect = 2e-13
 Identities = 44/232 (18%), Positives = 77/232 (33%), Gaps = 81/232 (34%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           +  + +  LP ++  EE +  F + GE+ S   V  ++T +  G GF+ +   + A  A+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 485 SASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTP 544
           +        G+ L+ + + V  A            +  + +    NLY            
Sbjct: 62  NTLN-----GLRLQTKTIKVSYA------------RPSSASIRDANLY------------ 92

Query: 545 AAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVS 604
                                                +  LPK+MT+K L++L       
Sbjct: 93  -------------------------------------VSGLPKTMTQKELEQLF------ 109

Query: 605 RASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN 656
               Q   I   + L     G       SRGV F+ F +   A  A++ LN 
Sbjct: 110 ---SQYGRIITSRILVDQVTGV------SRGVGFIRFDKRIEAEEAIKGLNG 152

>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 Length = 167

 Score = 65.3 bits (160), Expect = 1e-12
 Identities = 24/110 (21%), Positives = 50/110 (45%), Gaps = 7/110 (6%)

Query: 402 VSKLNSSKSKPKSLK----QTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVP 457
           ++ LN  + + K++K    +          +++  LP  +  +E++Q FS +G +++   
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120

Query: 458 VLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
           ++ QVT   +G GF++F     A  A+      +G         +TV  A
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKG---LNGQKPSGATEPITVKFA 167

>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 Length = 167

 Score = 49.9 bits (120), Expect = 2e-07
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
           +V  K + +  G+G+V +   +DA +A+   NG  +  + I V      A       +  
Sbjct: 34  LVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVS----YARPSSASIRDA 89

Query: 61  QEVQAEDIEKTMDNKD 76
             +    + KTM  K+
Sbjct: 90  -NLYVSGLPKTMTQKE 104

>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 Length = 167

 Score = 41.4 bits (98), Expect = 2e-04
 Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 21/84 (25%)

Query: 576 SRTRLVIYNLPKSMTEKGLKKLCIDA--VVSRASKQKPVIKQIKFLQSLKKGKVDTK-HY 632
           S+T L++  LP++MT++  + L      + S         K ++          D     
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIES--------CKLVR----------DKITGQ 42

Query: 633 SRGVAFVEFTEHQHALVALRVLNN 656
           S G  FV + + + A  A+  LN 
Sbjct: 43  SLGYGFVNYIDPKDAEKAINTLNG 66

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 80.8 bits (200), Expect = 1e-18
 Identities = 23/98 (23%), Positives = 47/98 (47%), Gaps = 4/98 (4%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G      +   L++ N+ + A    ++++F        + +P N   G SKG+AF++F  
Sbjct: 7   GNSTWSGESKTLVLSNLSYSATEETLQEVFEKAT---FIKVPQN-QNGKSKGYAFIEFAS 62

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAA 305
             DA+ A+   N ++   R I ++   P+   +SG ++
Sbjct: 63  FEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSS 100

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 18/101 (17%), Positives = 38/101 (37%), Gaps = 11/101 (10%)

Query: 410 SKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGT 469
           S   S   T   +    T+ + NL +    E +++ F     +     V      + KG 
Sbjct: 2   SSGSSGNSTWSGES--KTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGY 55

Query: 470 GFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
            F++F + E A  A+++          ++GR + +     +
Sbjct: 56  AFIEFASFEDAKEALNSCN-----KREIEGRAIRLELQGPR 91

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 50.0 bits (120), Expect = 7e-08
 Identities = 15/56 (26%), Positives = 27/56 (48%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          V +  + + +G+ +++FA  EDA  A+   N   + GR I ++    R S     S
Sbjct: 44 VPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPS 99

>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 Length = 129

 Score = 81.7 bits (202), Expect = 1e-18
 Identities = 25/94 (26%), Positives = 48/94 (51%)

Query: 203 WARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAF 262
            +R +G   +      L +  +       +++++FS  G + +V I ++  +  S+GFAF
Sbjct: 33  GSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 92

Query: 263 VKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           V F    DA+ A ++ NG +   R I VD+++ K
Sbjct: 93  VYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126

>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 Length = 129

 Score = 70.5 bits (173), Expect = 9e-15
 Identities = 19/106 (17%), Positives = 42/106 (39%), Gaps = 5/106 (4%)

Query: 406 NSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKR 465
                +           +    + +  L       ++++ FS +G +     V  Q ++R
Sbjct: 27  GQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR 86

Query: 466 PKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
            +G  F+ F+ V+ A  A   +      G+ L GR++ V  ++ K+
Sbjct: 87  SRGFAFVYFENVDDAKEAKERAN-----GMELDGRRIRVDFSITKR 127

>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 Length = 129

 Score = 52.0 bits (125), Expect = 2e-08
 Identities = 17/49 (34%), Positives = 27/49 (55%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
           +V  + S   RGF +V F  ++DA  A E  NG  + GR+I V  ++ +
Sbjct: 78  IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 80.0 bits (198), Expect = 2e-18
 Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 1/88 (1%)

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
              +  +K KL I  +PF     E++++    G V ++ +  N   G  KG A+V++  +
Sbjct: 10  RYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENE 68

Query: 269 RDAESAIQKFNGQKFGKRPIAVDWAVPK 296
             A  A+ K +G    +  I V  +   
Sbjct: 69  SQASQAVMKMDGMTIKENIIKVAISNSG 96

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 68.1 bits (167), Expect = 3e-14
 Identities = 21/104 (20%), Positives = 43/104 (41%), Gaps = 8/104 (7%)

Query: 408 SKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPK 467
           S       + +   ++  + +FI  LPF    EE+++   A G V     V ++   +PK
Sbjct: 2   SSGSSGVFRYSTSLEK--HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPK 58

Query: 468 GTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           G  +++++    A+ AV         G+ +K   + V  +    
Sbjct: 59  GLAYVEYENESQASQAVMKMD-----GMTIKENIIKVAISNSGP 97

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 46.5 bits (111), Expect = 9e-07
 Identities = 10/41 (24%), Positives = 19/41 (46%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRAS 51
          +G  YV++     A++AV   +G ++    I V  +    S
Sbjct: 58 KGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPS 98

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 79.6 bits (197), Expect = 2e-18
 Identities = 25/97 (25%), Positives = 44/97 (45%), Gaps = 8/97 (8%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G  GS     KL I N+      ++++ +F          +P      L  G+AFV +  
Sbjct: 1   GSSGSSGMN-KLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPD 53

Query: 268 KRDAESAIQKFNGQ-KFGKRPIAVDWAVPKNIYSSGG 303
           +  A  AI+  +G+ +   + + VD++V K + SSG 
Sbjct: 54  QNWAIRAIETLSGKVELHGKIMEVDYSVSKKLRSSGP 90

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 53.0 bits (128), Expect = 4e-09
 Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 10/86 (11%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           N ++I NL   +  ++++Q F      ++             G  F+ +     A  A+ 
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLA------GQVLLKSGYAFVDYPDQNWAIRAI- 61

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKK 511
             +T SG  + L G+ + V  ++ KK
Sbjct: 62  --ETLSG-KVELHGKIMEVDYSVSKK 84

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 11/58 (18%), Positives = 25/58 (43%), Gaps = 4/58 (6%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTS-VGGRKIGVKHAMHRASLEQRRS 57
          +          G+ +V +     A RA+E  +G   + G+ + V +++ +   + R S
Sbjct: 34 LPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK---KLRSS 88

>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 Length = 99

 Score = 79.6 bits (197), Expect = 2e-18
 Identities = 24/97 (24%), Positives = 43/97 (44%), Gaps = 6/97 (6%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           GGE + TQ+ +L + N+P      E++ +F   G    V+I         KGF F++   
Sbjct: 7   GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFIRLET 60

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGA 304
           +  AE A  + +      + + V +A      +SG +
Sbjct: 61  RTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPS 97

>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 Length = 99

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 15/88 (17%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVS-FVPVLHQVTKRPKGTGFLKFKTVEAATAA 483
           ++ +F+ NLP D+  EE+++ F  +G+    F+        + KG GF++ +T   A  A
Sbjct: 15  RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-------KDKGFGFIRLETRTLAEIA 67

Query: 484 VSASKTTSGL-GIFLKGRQLTVLKALDK 510
                    L  + L+G+QL V  A   
Sbjct: 68  KVE------LDNMPLRGKQLRVRFACHS 89

>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 Length = 99

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 13/47 (27%), Positives = 23/47 (48%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          +GFG+++      A  A    +   + G+++ V+ A H ASL    S
Sbjct: 51 KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPS 97

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 82.8 bits (205), Expect = 2e-18
 Identities = 41/236 (17%), Positives = 75/236 (31%), Gaps = 67/236 (28%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFV-----PVLHQVTKRPKGTGFLKFKTVEAA 480
             +++ N+PF +  E +   F+A   +         PVL     + K   FL+F++V+  
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 481 TAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLIL 540
           T A++        GI  +G+ L +      +  HD +     +E                
Sbjct: 65  TQAMAFD------GIIFQGQSLKI------RRPHDYQPLPGMSENPSVYV---------- 102

Query: 541 EGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCID 600
                                      + S     S  +L I  LP  + +  +K+L   
Sbjct: 103 -------------------------PGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELL-- 135

Query: 601 AVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN 656
                       +K    ++    G       S+G AF E+ +      A+  LN 
Sbjct: 136 -------TSFGPLKAFNLVKDSATGL------SKGYAFCEYVDINVTDQAIAGLNG 178

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 76.2 bits (188), Expect = 5e-16
 Identities = 21/79 (26%), Positives = 39/79 (49%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL I  +P     +++K++ +  G +    +  ++ TGLSKG+AF ++      + AI  
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175

Query: 278 FNGQKFGKRPIAVDWAVPK 296
            NG + G + + V  A   
Sbjct: 176 LNGMQLGDKKLLVQRASVG 194

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 74.7 bits (184), Expect = 2e-15
 Identities = 24/116 (20%), Positives = 51/116 (43%), Gaps = 7/116 (6%)

Query: 393 VNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEV 452
           +        +  ++ + S       +    +  + +FI  LP  L++++VK+  ++FG +
Sbjct: 82  IRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPL 141

Query: 453 VSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGL-GIFLKGRQLTVLKA 507
            +F  V    T   KG  F ++  +     A+      +GL G+ L  ++L V +A
Sbjct: 142 KAFNLVKDSATGLSKGYAFCEYVDINVTDQAI------AGLNGMQLGDKKLLVQRA 191

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 67.0 bits (164), Expect = 6e-13
 Identities = 18/104 (17%), Positives = 34/104 (32%), Gaps = 6/104 (5%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPH-----NTDTGLSKGFAFVKFTCKRDAE 272
           +L + NIPF      + D F+    +  +                K FAF++F    +  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 273 SAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNS 316
            A+  F+G  F  + + +                 V   G  ++
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVST 108

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 50.4 bits (121), Expect = 3e-07
 Identities = 9/46 (19%), Positives = 24/46 (52%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           +V    +   +G+ + ++  +   ++A+   NG  +G +K+ V+ A
Sbjct: 146 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 50.0 bits (120), Expect = 4e-07
 Identities = 10/73 (13%), Positives = 27/73 (36%), Gaps = 1/73 (1%)

Query: 2   VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQ 61
           V     N+ + F +++F  +++  +A+   +G    G+ + ++       L       + 
Sbjct: 42  VLAVQINQDKNFAFLEFRSVDETTQAMAF-DGIIFQGQSLKIRRPHDYQPLPGMSENPSV 100

Query: 62  EVQAEDIEKTMDN 74
            V         D+
Sbjct: 101 YVPGVVSTVVPDS 113

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 81.0 bits (200), Expect = 2e-18
 Identities = 28/98 (28%), Positives = 42/98 (42%)

Query: 196 EIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTG 255
           E           G  GS T K  L +  +  +     +   F P G + ++ IP + +T 
Sbjct: 43  ERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETE 102

Query: 256 LSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA 293
             +GFAFV+F    DA +AI   N  +   R I V+ A
Sbjct: 103 KHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 64.4 bits (157), Expect = 2e-12
 Identities = 20/94 (21%), Positives = 40/94 (42%), Gaps = 5/94 (5%)

Query: 414 SLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLK 473
               + G    +  +++  L  ++D++ +   F  FG++      L   T++ +G  F++
Sbjct: 52  GSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 111

Query: 474 FKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
           F+  E A AA+            L GR + V  A
Sbjct: 112 FELAEDAAAAIDNMN-----ESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 49.8 bits (119), Expect = 2e-07
 Identities = 16/46 (34%), Positives = 26/46 (56%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           +     + +HRGF +V+F + EDA  A++  N + + GR I V  A
Sbjct: 95  IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>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 Length = 106

 Score = 79.7 bits (197), Expect = 3e-18
 Identities = 26/92 (28%), Positives = 41/92 (44%), Gaps = 7/92 (7%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL I  IP      ++K +F   G ++ + +  +  TG+ KG AF+ +  +  A  A   
Sbjct: 15  KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74

Query: 278 FNGQK---FGKRPIAVDWAVPK----NIYSSG 302
            + QK      RPI V  A  +    +  SSG
Sbjct: 75  LHEQKTLPGMNRPIQVKPADSESRGGSGPSSG 106

>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 Length = 106

 Score = 61.6 bits (150), Expect = 7e-12
 Identities = 26/94 (27%), Positives = 41/94 (43%), Gaps = 8/94 (8%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
           +D     +FI  +P +LD +++K  F  FG++     +  + T   KG  FL +   E+A
Sbjct: 9   KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68

Query: 481 TAAVSA---SKTTSGLGIFLKGRQLTVLKALDKK 511
             A SA    KT  G       R + V  A  + 
Sbjct: 69  LKAQSALHEQKTLPG-----MNRPIQVKPADSES 97

>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 Length = 106

 Score = 41.9 bits (99), Expect = 5e-05
 Identities = 11/56 (19%), Positives = 20/56 (35%), Gaps = 3/56 (5%)

Query: 5   KGSNEHRGFGYVQFAVMEDANRAVEMKNGTSV---GGRKIGVKHAMHRASLEQRRS 57
           + +  H+G  ++ +   E A +A    +         R I VK A   +      S
Sbjct: 49  RFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSGPS 104

>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 Length = 106

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 15/81 (18%)

Query: 576 SRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRG 635
              +L I  +P+++ EK LK L          K    I ++  L+    G        +G
Sbjct: 12  DAIKLFIGQIPRNLDEKDLKPLF-----EEFGK----IYELTVLKDRFTGM------HKG 56

Query: 636 VAFVEFTEHQHALVALRVLNN 656
            AF+ + E + AL A   L+ 
Sbjct: 57  CAFLTYCERESALKAQSALHE 77

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 79.7 bits (197), Expect = 3e-18
 Identities = 18/93 (19%), Positives = 30/93 (32%), Gaps = 3/93 (3%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           GG+    +   +    +    +   +KDM    G V  V I  +  T    G A V FT 
Sbjct: 1   GGQIPLKE---VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTS 57

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYS 300
            R A+  ++  +        I     +      
Sbjct: 58  TRGAKETVKNLHLTSVMGNIIHAQLDIKGQQRM 90

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 69.3 bits (170), Expect = 1e-14
 Identities = 13/80 (16%), Positives = 25/80 (31%), Gaps = 5/80 (6%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
              +    L  ++    +K     +GEV     +LH  T++  G   + F +   A   V
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 485 SASKTTSGLGIFLKGRQLTV 504
                       + G  +  
Sbjct: 66  KNLH-----LTSVMGNIIHA 80

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 53.9 bits (130), Expect = 3e-09
 Identities = 11/60 (18%), Positives = 21/60 (35%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
          ++    + +H G   V F     A   V+  + TSV G  I  +  +      +    + 
Sbjct: 38 ILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIV 97

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 38.5 bits (90), Expect = 8e-04
 Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 15/79 (18%)

Query: 578 TRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVA 637
             +    L  ++ E  LK +C         ++   +++++ L   +  K        G+A
Sbjct: 7   KEVTFARLNDNVRETFLKDMC---------RKYGEVEEVEILLHPRTRK------HLGLA 51

Query: 638 FVEFTEHQHALVALRVLNN 656
            V FT  + A   ++ L+ 
Sbjct: 52  RVLFTSTRGAKETVKNLHL 70

>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 Length = 115

 Score = 79.7 bits (197), Expect = 3e-18
 Identities = 28/99 (28%), Positives = 46/99 (46%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G +    +   L I ++P +    ++  MF P G V +  +  +  T LSK F FV +  
Sbjct: 17  GSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN 76

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAA 306
              A++AIQ  NG + G + + V     KN   SG ++ 
Sbjct: 77  PVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPSSG 115

>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 Length = 115

 Score = 60.4 bits (147), Expect = 2e-11
 Identities = 23/103 (22%), Positives = 45/103 (43%), Gaps = 7/103 (6%)

Query: 403 SKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQV 462
           S  +    +      ++ E      +FI +LP +  ++++ Q F  FG VVS    + + 
Sbjct: 3   SGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ 62

Query: 463 TKRPKGTGFLKFKTVEAATAAVSASKTTSGL-GIFLKGRQLTV 504
           T   K  GF+ +    +A AA+ +      + G  +  ++L V
Sbjct: 63  TNLSKCFGFVSYDNPVSAQAAIQS------MNGFQIGMKRLKV 99

>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 Length = 115

 Score = 45.4 bits (108), Expect = 3e-06
 Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 3/54 (5%)

Query: 5   KGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
           K +N  + FG+V +     A  A++  NG  +G +++ V+    +      +S 
Sbjct: 61  KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSK---NDSKSG 111

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 79.2 bits (196), Expect = 4e-18
 Identities = 28/98 (28%), Positives = 46/98 (46%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G  G  + + KL +  + F      ++ +FS  G +  V +  + +T  S+GF FV F  
Sbjct: 4   GSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN 63

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAA 305
             DA+ A+   NG+    R I VD A   +   SG ++
Sbjct: 64  IDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSS 101

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 67.7 bits (166), Expect = 4e-14
 Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 5/91 (5%)

Query: 420 GEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
           G    +  +F+  L FD + + ++Q FS +G++   V V  + T+R +G GF+ F+ ++ 
Sbjct: 7   GMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDD 66

Query: 480 ATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
           A  A+ A       G  + GRQ+ V +A   
Sbjct: 67  AKDAMMAMN-----GKSVDGRQIRVDQAGKS 92

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 52.2 bits (126), Expect = 9e-09
 Identities = 19/51 (37%), Positives = 28/51 (54%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRAS 51
          +V  + +   RGFG+V F  ++DA  A+   NG SV GR+I V  A   + 
Sbjct: 44 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD 94

>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 Length = 105

 Score = 79.2 bits (196), Expect = 4e-18
 Identities = 26/95 (27%), Positives = 45/95 (47%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G    + Q   + +  +  K     + ++F   G V N ++P +  TG  +G+ FV+F  
Sbjct: 7   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 66

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSG 302
           + DA+ AI+  +  K   +PI V+ A   N   SG
Sbjct: 67  EEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101

>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 Length = 105

 Score = 60.4 bits (147), Expect = 2e-11
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 7/92 (7%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
           E     T+++  L   +    + + F   G VV+      +VT + +G GF++F + E A
Sbjct: 11  ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70

Query: 481 TAAVSASKTTSGL-GIFLKGRQLTVLKALDKK 511
             A+        +  I L G+ + V KA    
Sbjct: 71  DYAIKI------MDMIKLYGKPIRVNKASAHN 96

>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 Length = 105

 Score = 50.3 bits (121), Expect = 6e-08
 Identities = 15/57 (26%), Positives = 29/57 (50%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           M   + + +H+G+G+V+F   EDA+ A+++ +   + G+ I V  A          S
Sbjct: 47  MPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPS 103

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 78.3 bits (194), Expect = 5e-18
 Identities = 23/79 (29%), Positives = 37/79 (46%)

Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
            K  L +  +  +     +   F P G + ++ IP + +T   +GFAFV+F    DA +A
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

Query: 275 IQKFNGQKFGKRPIAVDWA 293
           I   N  +   R I V+ A
Sbjct: 66  IDNMNESELFGRTIRVNLA 84

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 61.4 bits (150), Expect = 4e-12
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             +++  L  ++D++ +   F  FG++      L   T++ +G  F++F+  E A AA+ 
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 486 ASKTTSGLGIFLKGRQLTVLKA 507
                      L GR + V  A
Sbjct: 68  NMN-----ESELFGRTIRVNLA 84

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 48.3 bits (116), Expect = 1e-07
 Identities = 16/46 (34%), Positives = 26/46 (56%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          +     + +HRGF +V+F + EDA  A++  N + + GR I V  A
Sbjct: 39 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 81.1 bits (201), Expect = 5e-18
 Identities = 22/123 (17%), Positives = 55/123 (44%), Gaps = 10/123 (8%)

Query: 177 VLYTTVKSACASVALLHQKEIKGGTV---WARQLGGEGSKTQKWKLIIRNIPFKAKVNEI 233
           V + + +    ++ L    ++ G  +     +    +  +  +  L+ +N+ F    +E+
Sbjct: 59  VDFESAEDLEKALEL-TGLKVFGNEIKLEKPKGRDSKKVRAAR-TLLAKNLSFNITEDEL 116

Query: 234 KDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA 293
           K++F     +  V     +  G SKG A+++F  + DAE  +++  G +   R +++ + 
Sbjct: 117 KEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT 171

Query: 294 VPK 296
             K
Sbjct: 172 GEK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 70.3 bits (173), Expect = 3e-14
 Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 2/85 (2%)

Query: 213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAE 272
            T  + L I N+     V E+K   S +    ++ +     TG ++ F +V F    D E
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLE 68

Query: 273 SAIQKFNGQKFGKRPIAVDWAVPKN 297
            A++   G K     I ++    ++
Sbjct: 69  KALE-LTGLKVFGNEIKLEKPKGRD 92

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 68.8 bits (169), Expect = 1e-13
 Identities = 37/237 (15%), Positives = 70/237 (29%), Gaps = 86/237 (36%)

Query: 420 GEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
            E      +FI NL  +    E+K   S        + V+   T   +  G++ F++ E 
Sbjct: 8   SESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAED 66

Query: 480 ATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLI 539
              A+  +      G+ + G ++ +          +K   +   +    R L        
Sbjct: 67  LEKALELT------GLKVFGNEIKL----------EKPKGRDSKKVRAARTLL------- 103

Query: 540 LEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCI 599
                                                       NL  ++TE  LK++  
Sbjct: 104 ------------------------------------------AKNLSFNITEDELKEVFE 121

Query: 600 DAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN 656
           DA+            +I+ +   + GK      S+G+A++EF     A   L     
Sbjct: 122 DAL------------EIRLVS--QDGK------SKGIAYIEFKSEADAEKNLEEKQG 158

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 63.4 bits (155), Expect = 7e-12
 Identities = 20/110 (18%), Positives = 44/110 (40%), Gaps = 14/110 (12%)

Query: 401 DVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLH 460
             +++   K K +  K+         T+   NL F++  +E+K+ F    E+        
Sbjct: 79  FGNEIKLEKPKGRDSKKVRA----ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ--- 131

Query: 461 QVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
               + KG  +++FK+   A   +   +     G  + GR +++    +K
Sbjct: 132 --DGKSKGIAYIEFKSEADAEKNLEEKQ-----GAEIDGRSVSLYYTGEK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 53.8 bits (130), Expect = 1e-08
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 2   VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
           V    +  +R FGYV F   ED  +A+E+  G  V G +I ++    R S + R ++
Sbjct: 45  VVDVRTGTNRKFGYVDFESAEDLEKALEL-TGLKVFGNEIKLEKPKGRDSKKVRAAR 100

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 51.5 bits (124), Expect = 8e-08
 Identities = 10/40 (25%), Positives = 20/40 (50%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRA 50
           +G  Y++F    DA + +E K G  + GR + + +   + 
Sbjct: 136 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 175

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 78.4 bits (194), Expect = 6e-18
 Identities = 30/94 (31%), Positives = 40/94 (42%), Gaps = 2/94 (2%)

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
           G    +   ++ +RN+PF      +KD F+  G V    I    + G SKG   VKF   
Sbjct: 1   GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESP 58

Query: 269 RDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSG 302
             AE A +  NG K   R I V      +  SSG
Sbjct: 59  EVAERACRMMNGMKLSGREIDVRIDRNASGPSSG 92

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 62.6 bits (153), Expect = 2e-12
 Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 13/96 (13%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             IF+ NLPFD   + +K +F+  G V+     +     + KG G +KF++ E A  A  
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYA--DIKMENGKSKGCGVVKFESPEVAERACR 66

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKS 521
                   G+ L GR++ V      ++  +     S
Sbjct: 67  MMN-----GMKLSGREIDV------RIDRNASGPSS 91

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 50.3 bits (121), Expect = 4e-08
 Identities = 15/39 (38%), Positives = 21/39 (53%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
          +G G V+F   E A RA  M NG  + GR+I V+   + 
Sbjct: 48 KGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNA 86

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 78.5 bits (194), Expect = 8e-18
 Identities = 20/85 (23%), Positives = 36/85 (42%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L ++N+  +    ++  +F+         I     TG  +G AF+ F  K  A  A+  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSG 302
            NG K   + + +++   K   SSG
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQRSSG 111

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 60.4 bits (147), Expect = 2e-11
 Identities = 19/86 (22%), Positives = 33/86 (38%), Gaps = 5/86 (5%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             +++ NL   +   ++   F+ F E          +T R +G  F+ F   E A  A+ 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKK 511
                   G  L G+ L +    +KK
Sbjct: 86  LVN-----GYKLYGKILVIEFGKNKK 106

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 41.5 bits (98), Expect = 8e-05
 Identities = 9/43 (20%), Positives = 22/43 (51%)

Query: 7   SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
           +   RG  ++ F   E A +A+ + NG  + G+ + ++   ++
Sbjct: 63  TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNK 105

>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 Length = 111

 Score = 78.7 bits (194), Expect = 8e-18
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 7/84 (8%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           ++ +N+P      EI++ FS  G +  V +P           A V+F    +A  A +  
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHL 66

Query: 279 NGQKFGKRPIAVDWAVPKNIYSSG 302
              KF   P+ ++WA P  ++ + 
Sbjct: 67  AYSKFHHVPLYLEWA-PIGVFGAA 89

>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 Length = 111

 Score = 45.6 bits (108), Expect = 3e-06
 Identities = 17/101 (16%), Positives = 28/101 (27%), Gaps = 11/101 (10%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             I   NLP      E+++ FS FG +         +      T  ++F     A  A  
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRV------LLPEGGITAIVEFLEPLEARKAFR 64

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETN 526
                           L +  A         +   S++E  
Sbjct: 65  HLA-----YSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQP 100

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 76.6 bits (189), Expect = 2e-17
 Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 4/84 (4%)

Query: 208 GGEGSK-TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFT 266
           G  GS  T    + +R  PF      + +  +P+  V  + I  N   G   G+ FV F+
Sbjct: 1   GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAH-GNKTGYIFVDFS 58

Query: 267 CKRDAESAIQKFNGQKFGKRPIAV 290
            + + + A++  N +  G R I V
Sbjct: 59  NEEEVKQALKC-NREYMGGRYIEV 81

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 52.3 bits (126), Expect = 7e-09
 Identities = 13/90 (14%), Positives = 33/90 (36%), Gaps = 8/90 (8%)

Query: 418 TEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTV 477
           +       +T+ +   PF++  + V +  +    V   + ++        G  F+ F   
Sbjct: 3   SGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV--AIRIVRNAHGNKTGYIFVDFSNE 60

Query: 478 EAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
           E    A+  ++       ++ GR + V + 
Sbjct: 61  EEVKQALKCNRE------YMGGRYIEVFRE 84

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 4  KKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
          +       G+ +V F+  E+  +A++  N   +GGR I V
Sbjct: 43 RNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEV 81

>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} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 77.0 bits (190), Expect = 3e-17
 Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 3/80 (3%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
             L IRN+P+K    E+ D+F   G +  + +    +T  ++G A+V +    DA++A+ 
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNAVD 65

Query: 277 KFNGQKFGKRPIAVDWAVPK 296
             +G     R + V +    
Sbjct: 66  HLSGFNVSNRYLVVLYYNAN 85

>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} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 65.9 bits (161), Expect = 3e-13
 Identities = 21/106 (19%), Positives = 40/106 (37%), Gaps = 8/106 (7%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            ++I NLP+ +  EE+   F  +G +          T   +GT ++ ++ +  A  AV  
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNAVDH 66

Query: 487 SKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLY 532
                  G  +  R L VL     +     +  K + +    +  Y
Sbjct: 67  LS-----GFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKY 107

>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} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 50.4 bits (121), Expect = 6e-08
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 9   EHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAEDI 68
           E RG  YV +  + DA  AV+  +G +V  R + V +     + ++  +K  +E Q + +
Sbjct: 45  ETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEE-QLKLL 103

Query: 69  EKTMDNKDGVISGAEK 84
           ++    K G+ +   K
Sbjct: 104 KE----KYGINTDPPK 115

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 77.0 bits (190), Expect = 3e-17
 Identities = 19/79 (24%), Positives = 44/79 (55%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L + ++ F    + ++ +F P G + ++ +  +++TG SKG+ F+ F+    A+ A+++
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87

Query: 278 FNGQKFGKRPIAVDWAVPK 296
            NG +   RP+ V     +
Sbjct: 88  LNGFELAGRPMKVGHVTER 106

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 63.1 bits (154), Expect = 2e-12
 Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 7/86 (8%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            +++ +L F++  + ++  F  FG + S   ++   T R KG GF+ F   E A  A+  
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87

Query: 487 SKTTSGL-GIFLKGRQLTVLKALDKK 511
                 L G  L GR + V    ++ 
Sbjct: 88  ------LNGFELAGRPMKVGHVTERT 107

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 50.0 bits (120), Expect = 9e-08
 Identities = 14/49 (28%), Positives = 26/49 (53%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
           ++    +   +G+G++ F+  E A +A+E  NG  + GR + V H   R
Sbjct: 58  LMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER 106

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 77.0 bits (190), Expect = 3e-17
 Identities = 26/110 (23%), Positives = 45/110 (40%), Gaps = 2/110 (1%)

Query: 184 SACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLV 243
           ++  S + L    +      A   G +    +   L I ++P +    ++   F P G V
Sbjct: 10  ASALSTSPLASVALSAA--AAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNV 67

Query: 244 WNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA 293
            +  +  +  T LSK F FV F     A+ AI+  NG + G + + V   
Sbjct: 68  ISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 62.4 bits (152), Expect = 4e-12
 Identities = 21/97 (21%), Positives = 41/97 (42%), Gaps = 7/97 (7%)

Query: 409 KSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKG 468
            +   +    + E      +FI +LP +  + ++   F  FG V+S    + + T   K 
Sbjct: 24  SAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKC 83

Query: 469 TGFLKFKTVEAATAAVSASKTTSGL-GIFLKGRQLTV 504
            GF+ F   ++A  A+ A      + G  +  ++L V
Sbjct: 84  FGFVSFDNPDSAQVAIKA------MNGFQVGTKRLKV 114

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 45.1 bits (107), Expect = 5e-06
 Identities = 12/42 (28%), Positives = 23/42 (54%)

Query: 5   KGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           K ++  + FG+V F   + A  A++  NG  VG +++ V+  
Sbjct: 76  KQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 76.2 bits (188), Expect = 4e-17
 Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L+ +N+ F    +E+K++F     +  V     +  G SKG A+++F  + DAE  +++
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 278 FNGQKFGKRPIAVDWAVPK 296
             G +   R +++ +   K
Sbjct: 73  KQGAEIDGRSVSLYYTGEK 91

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 61.1 bits (149), Expect = 7e-12
 Identities = 17/90 (18%), Positives = 37/90 (41%), Gaps = 10/90 (11%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
           +     T+   NL F++  +E+K+ F    E+            + KG  +++FK+   A
Sbjct: 12  KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADA 66

Query: 481 TAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
              +   +     G  + GR +++    +K
Sbjct: 67  EKNLEEKQ-----GAEIDGRSVSLYYTGEK 91

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 10/40 (25%), Positives = 20/40 (50%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRA 50
          +G  Y++F    DA + +E K G  + GR + + +   + 
Sbjct: 53 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 92

>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 Length = 103

 Score = 76.2 bits (188), Expect = 4e-17
 Identities = 31/97 (31%), Positives = 50/97 (51%), Gaps = 2/97 (2%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G   SK+   +L + NIPF+ +  +++ MF   G + +V I    +   SKGF FV F  
Sbjct: 7   GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFEN 64

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGA 304
             DA+ A +K +G     R I V+ A  + + +SG +
Sbjct: 65  SADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPS 101

>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 Length = 103

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 7/85 (8%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + + N+PF   + +++Q F  FG+++    + +   +  KG GF+ F+    A  A  
Sbjct: 16  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRARE 73

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDK 510
                   G  ++GR++ V  A  +
Sbjct: 74  KLH-----GTVVEGRKIEVNNATAR 93

>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 Length = 103

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 21/48 (43%), Positives = 26/48 (54%)

Query: 10  HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
            +GFG+V F    DA+RA E  +GT V GRKI V +A  R       S
Sbjct: 54  SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPS 101

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 76.3 bits (188), Expect = 5e-17
 Identities = 22/107 (20%), Positives = 47/107 (43%), Gaps = 8/107 (7%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLV--------WNVYIPHNTDTGLSKG 259
           G     +    + ++ +     ++++ D F   G+V          ++I  + +TG  KG
Sbjct: 7   GDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKG 66

Query: 260 FAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAA 306
            A V +     A++A++ F+G+ F    + V  A  K   +SG ++ 
Sbjct: 67  DATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSSG 113

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 58.2 bits (141), Expect = 1e-10
 Identities = 19/99 (19%), Positives = 37/99 (37%), Gaps = 16/99 (16%)

Query: 419 EGEDELQNT-IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQV--------TKRPKGT 469
           + +++  N+ I++  L   +  +++   F   G V         +        T +PKG 
Sbjct: 8   DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 67

Query: 470 GFLKFKTVEAATAAVSASKTTSGL-GIFLKGRQLTVLKA 507
             + ++    A AAV          G   +G +L V  A
Sbjct: 68  ATVSYEDPPTAKAAVEW------FDGKDFQGSKLKVSLA 100

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 43.2 bits (102), Expect = 2e-05
 Identities = 13/57 (22%), Positives = 22/57 (38%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           +   K + + +G   V +     A  AVE  +G    G K+ V  A  +  +    S
Sbjct: 55  IYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPS 111

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 75.7 bits (187), Expect = 5e-17
 Identities = 21/76 (27%), Positives = 38/76 (50%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L +  +       +++++FS  G + +V I ++  +  S+GFAFV F    DA+ A ++
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76

Query: 278 FNGQKFGKRPIAVDWA 293
            NG +   R I V   
Sbjct: 77  ANGMELDGRRIRVSGP 92

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 64.1 bits (157), Expect = 6e-13
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 5/82 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + +  L       ++++ FS +G +     V  Q ++R +G  F+ F+ V+ A  A  
Sbjct: 16  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75

Query: 486 ASKTTSGLGIFLKGRQLTVLKA 507
            +      G+ L GR++ V   
Sbjct: 76  RAN-----GMELDGRRIRVSGP 92

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 51.0 bits (123), Expect = 3e-08
 Identities = 17/46 (36%), Positives = 24/46 (52%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          +V  + S   RGF +V F  ++DA  A E  NG  + GR+I V   
Sbjct: 47 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGP 92

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 79.3 bits (196), Expect = 6e-17
 Identities = 37/240 (15%), Positives = 82/240 (34%), Gaps = 70/240 (29%)

Query: 417 QTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKT 476
           Q +G   + + +++ ++ ++L  + ++Q F+ FG + S       VT + KG  F++++ 
Sbjct: 20  QRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEV 79

Query: 477 VEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKE 536
            EAA  A+          + L GR + V +  +        ID+   E      +Y+A  
Sbjct: 80  PEAAQLALEQMN-----SVMLGGRNIKVGRPSNIG-QAQPIIDQLAEEARAFNRIYVA-- 131

Query: 537 GLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKK 596
                                                          ++ + +++  +K 
Sbjct: 132 -----------------------------------------------SVHQDLSDDDIKS 144

Query: 597 LCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN 656
           +          +    IK     +    GK       +G  F+E+ + Q +  A+  +N 
Sbjct: 145 VF---------EAFGKIKSATLARDPTTGK------HKGYGFIEYEKAQSSQDAVSSMNL 189

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 78.1 bits (193), Expect = 1e-16
 Identities = 23/115 (20%), Positives = 47/115 (40%), Gaps = 6/115 (5%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++ + +I ++   + I+  F+P G + ++ +  ++ T   KGFAFV++     A+ A+++
Sbjct: 30  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGN------SDSGSDDDLGD 326
            N    G R I V                  + +              SDDD+  
Sbjct: 90  MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKS 144

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 76.2 bits (188), Expect = 6e-16
 Identities = 20/131 (15%), Positives = 52/131 (39%), Gaps = 11/131 (8%)

Query: 177 VLYTTVKSACASVALLHQKEIKGGTV---WA-----RQLGGEGSKTQKW---KLIIRNIP 225
           V Y   ++A  ++  ++   + G  +           Q   +    +     ++ + ++ 
Sbjct: 75  VEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVH 134

Query: 226 FKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK 285
                ++IK +F   G + +  +  +  TG  KG+ F+++   + ++ A+   N    G 
Sbjct: 135 QDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGG 194

Query: 286 RPIAVDWAVPK 296
           + + V  AV  
Sbjct: 195 QYLRVGKAVTP 205

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 73.9 bits (182), Expect = 3e-15
 Identities = 27/110 (24%), Positives = 52/110 (47%), Gaps = 5/110 (4%)

Query: 401 DVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLH 460
            V + ++       + Q   E    N I++ ++  DL ++++K  F AFG++ S      
Sbjct: 101 KVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARD 160

Query: 461 QVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
             T + KG GF++++  +++  AVS+          L G+ L V KA+  
Sbjct: 161 PTTGKHKGYGFIEYEKAQSSQDAVSSMN-----LFDLGGQYLRVGKAVTP 205

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 58.9 bits (143), Expect = 5e-10
 Identities = 17/62 (27%), Positives = 30/62 (48%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVT 60
           M     + +H+GF +V++ V E A  A+E  N   +GGR I V    +    +    ++ 
Sbjct: 60  MSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLA 119

Query: 61  QE 62
           +E
Sbjct: 120 EE 121

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 51.5 bits (124), Expect = 2e-07
 Identities = 10/43 (23%), Positives = 24/43 (55%)

Query: 7   SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
           + +H+G+G++++   + +  AV   N   +GG+ + V  A+  
Sbjct: 163 TGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 76.8 bits (189), Expect = 7e-17
 Identities = 29/101 (28%), Positives = 44/101 (43%), Gaps = 6/101 (5%)

Query: 193 HQKEIKGGTVWARQLGGEGSKTQK---WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIP 249
           H   + GG    R  G      Q      + +R +P+KA  N+I + FSP+  V  V+I 
Sbjct: 20  HMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIE 78

Query: 250 HNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
              D G   G A V+F    +A +A+ K +      R I +
Sbjct: 79  IGPD-GRVTGEADVEFATHEEAVAAMSK-DRANMQHRYIEL 117

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 54.1 bits (130), Expect = 6e-09
 Identities = 16/102 (15%), Positives = 34/102 (33%), Gaps = 8/102 (7%)

Query: 406 NSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKR 465
                +     +   +    + + +  LP+     ++   FS    V   V +      R
Sbjct: 27  GQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR--VHIEIGPDGR 84

Query: 466 PKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
             G   ++F T E A AA+S  +        ++ R + +   
Sbjct: 85  VTGEADVEFATHEEAVAAMSKDRA------NMQHRYIELFLN 120

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 41.4 bits (97), Expect = 1e-04
 Identities = 10/51 (19%), Positives = 19/51 (37%), Gaps = 5/51 (9%)

Query: 10  HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA----MHRASLEQRR 56
             G   V+FA  E+A  A+  K+  ++  R I +           +   + 
Sbjct: 85  VTGEADVEFATHEEAVAAMS-KDRANMQHRYIELFLNSTTGASNGAYSSQV 134

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 75.9 bits (187), Expect = 8e-17
 Identities = 23/106 (21%), Positives = 48/106 (45%), Gaps = 10/106 (9%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLV--------WNVYIPHNTDTGLSKGFAFVKFTCKR 269
            + ++ +     +  + D F  +G++          + +  + +TG  KG A V F    
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 270 DAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGA--AAGVQNKGD 313
            A++AI  F+G++F   PI V +A  +  ++ GG     G+++   
Sbjct: 69  SAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEHHHH 114

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 55.9 bits (135), Expect = 8e-10
 Identities = 20/95 (21%), Positives = 32/95 (33%), Gaps = 15/95 (15%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLH--------QVTKRPKGTGFLKFKTV 477
           NTIF+  L  ++  E V   F   G + +              + T + KG   + F   
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 478 EAATAAVSASKTTSGL-GIFLKGRQLTVLKALDKK 511
            +A AA+          G    G  + V  A  + 
Sbjct: 68  PSAKAAIDW------FDGKEFSGNPIKVSFATRRA 96

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 45.9 bits (109), Expect = 2e-06
 Identities = 13/58 (22%), Positives = 22/58 (37%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
           + T + + + +G   V F     A  A++  +G    G  I V  A  RA   +    
Sbjct: 47  LYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGN 104

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 77.2 bits (191), Expect = 1e-16
 Identities = 36/180 (20%), Positives = 76/180 (42%), Gaps = 24/180 (13%)

Query: 122 RTVIIGGLLNADMAEE-VHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASA---- 176
           R + +G L +  + E+ + +     G + ++   +  +            K + +     
Sbjct: 1   RVLYVGNL-DKAITEDILKQYFQVGGPIANIK--IMID------------KNNKNVNYAF 45

Query: 177 VLYTTVKSACASVALLHQKEIKGGTV---WARQLGGEGSKTQKWKLIIRNIPFKAKVNEI 233
           V Y     A  ++  L+ K+I+   V   WA Q   + S    + L + ++        +
Sbjct: 46  VEYHQSHDANIALQTLNGKQIENNIVKINWAFQ-SQQSSSDDTFNLFVGDLNVNVDDETL 104

Query: 234 KDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA 293
           ++ F       + ++  +  TG S+G+ FV FT + DA++A+    GQ    RP+ ++WA
Sbjct: 105 RNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 69.1 bits (170), Expect = 6e-14
 Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 1/87 (1%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + N+      + +K  F   G + N+ I  +     +  +AFV++    DA  A+Q  
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 279 NGQKFGKRPIAVDWAVPKNIYSSGGAA 305
           NG++     + ++WA      SS    
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTF 88

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 64.5 bits (158), Expect = 3e-12
 Identities = 22/101 (21%), Positives = 43/101 (42%), Gaps = 11/101 (10%)

Query: 404 KLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVT 463
           K+N +    +S             +F+ +L  ++D+E ++  F  F   +S   +    T
Sbjct: 72  KINWAFQSQQSSSDDTF------NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQT 125

Query: 464 KRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV 504
              +G GF+ F + + A  A+ + +     G  L GR L +
Sbjct: 126 GSSRGYGFVSFTSQDDAQNAMDSMQ-----GQDLNGRPLRI 161

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 55.6 bits (135), Expect = 3e-09
 Identities = 28/230 (12%), Positives = 63/230 (27%), Gaps = 80/230 (34%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            +++ NL   +  + +KQ F   G + + + ++     +     F+++     A  A+  
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIAN-IKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60

Query: 487 SKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAA 546
                  G  ++   + +  A        ++         D  NL+              
Sbjct: 61  LN-----GKQIENNIVKINWA-----FQSQQSSSD-----DTFNLF-------------- 91

Query: 547 EGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRA 606
                                              + +L  ++ ++ L+           
Sbjct: 92  -----------------------------------VGDLNVNVDDETLRNAF-------- 108

Query: 607 SKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN 656
            K  P       +  ++ G       SRG  FV FT    A  A+  +  
Sbjct: 109 -KDFPSYLSGHVMWDMQTGS------SRGYGFVSFTSQDDAQNAMDSMQG 151

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 47.1 bits (113), Expect = 2e-06
 Identities = 11/74 (14%), Positives = 31/74 (41%), Gaps = 11/74 (14%)

Query: 7   SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAE 66
           +N++  + +V++    DAN A++  NG  +    + +  A        +  + + +    
Sbjct: 37  NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWA-------FQSQQSSSDDTFN 89

Query: 67  ----DIEKTMDNKD 76
               D+   +D++ 
Sbjct: 90  LFVGDLNVNVDDET 103

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 46.0 bits (110), Expect = 6e-06
 Identities = 12/36 (33%), Positives = 20/36 (55%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           RG+G+V F   +DA  A++   G  + GR + +  A
Sbjct: 129 RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 75.0 bits (185), Expect = 1e-16
 Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 3/89 (3%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L ++ +        +K+ F          I  + +TG SKGF FV F  + DA++A + 
Sbjct: 17  TLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGGAAA 306
               +     + +DWA PK    SG ++ 
Sbjct: 74  MEDGEIDGNKVTLDWAKPKGEGGSGPSSG 102

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 60.3 bits (147), Expect = 2e-11
 Identities = 26/101 (25%), Positives = 40/101 (39%), Gaps = 10/101 (9%)

Query: 410 SKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGT 469
           S   S      +     T+F+  L  D   E +K+   +F   V    V  + T   KG 
Sbjct: 2   SSGSSGPNARSQPS--KTLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGF 56

Query: 470 GFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
           GF+ F + E A AA  A +        + G ++T+  A  K
Sbjct: 57  GFVDFNSEEDAKAAKEAME-----DGEIDGNKVTLDWAKPK 92

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 50.3 bits (121), Expect = 5e-08
 Identities = 16/57 (28%), Positives = 25/57 (43%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           +VT + +   +GFG+V F   EDA  A E      + G K+ +  A  +       S
Sbjct: 44  IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPS 100

>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} Length = 116

 Score = 75.4 bits (186), Expect = 1e-16
 Identities = 27/106 (25%), Positives = 44/106 (41%), Gaps = 3/106 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTD-TGLSKGFAFVKFTCKRDAESAIQ 276
           KL I  +  +     +K +F   G +  V +    D T  S+GFAF+ F    DA++A +
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLI--KDRTSKSRGFAFITFENPADAKNAAK 66

Query: 277 KFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDD 322
             NG+    + I V+ A   +  S G       ++    S S    
Sbjct: 67  DMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEHH 112

>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} Length = 116

 Score = 60.4 bits (147), Expect = 2e-11
 Identities = 19/90 (21%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
           E +    +FI  L  + + + +K  F   G +   V ++   T + +G  F+ F+    A
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISE-VLLIKDRTSKSRGFAFITFENPADA 61

Query: 481 TAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
             A          G  L G+ + V +A   
Sbjct: 62  KNAAKDMN-----GKSLHGKAIKVEQAKKP 86

>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} Length = 116

 Score = 52.7 bits (127), Expect = 1e-08
 Identities = 15/52 (28%), Positives = 26/52 (50%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
          +++ RGF ++ F    DA  A +  NG S+ G+ I V+ A   +     R +
Sbjct: 44 TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRR 95

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 74.8 bits (184), Expect = 1e-16
 Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 1/85 (1%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           +R +PF     EI   FS + +V N         G S G AFV+F  +  AE A++K + 
Sbjct: 20  LRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HK 78

Query: 281 QKFGKRPIAVDWAVPKNIYSSGGAA 305
           ++ G R I +  +    + +SG ++
Sbjct: 79  ERIGHRYIEIFKSSRAEVRTSGPSS 103

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 60.5 bits (147), Expect = 2e-11
 Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
              + +  LPF    EE+ Q FS    V + + +      R  G  F++F + E A  A+
Sbjct: 15  DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL 74

Query: 485 SASKTTSGLGIFLKGRQLTVLKA 507
              K        +  R + + K+
Sbjct: 75  KKHKE------RIGHRYIEIFKS 91

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          +         G  +VQFA  E A +A++ K+   +G R I +  +
Sbjct: 48 LPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS 91

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 77.6 bits (191), Expect = 1e-16
 Identities = 38/235 (16%), Positives = 77/235 (32%), Gaps = 56/235 (23%)

Query: 425 QNTIFICNL-PFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAA 483
            + + + NL P  +  + +   F  +G+V         +    K    ++      A  A
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVK-----ILFNKKENALVQMADGNQAQLA 57

Query: 484 VSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGT 543
           +S        G  L G+ + +       L+  + +   +    D                
Sbjct: 58  MSHLN-----GHKLHGKPIRI------TLSKHQNVQLPREGQED---------------Q 91

Query: 544 PAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVV 603
              +   +  + + +    K    +  P+       L + N+P S++E+ LK L      
Sbjct: 92  GLTKDYGNSPLHRFKKPGSKNFQNIFPPS-----ATLHLSNIPPSVSEEDLKVLF----- 141

Query: 604 SRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
              S    V+K  KF Q             R +A ++    + A+ AL  L+N+ 
Sbjct: 142 ---SSNGGVVKGFKFFQK-----------DRKMALIQMGSVEEAVQALIDLHNHD 182

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 58.4 bits (141), Expect = 6e-10
 Identities = 19/105 (18%), Positives = 37/105 (35%), Gaps = 4/105 (3%)

Query: 382 KGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEE 441
           K    Q   +   +     D       + K    K  +       T+ + N+P  +  E+
Sbjct: 77  KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEED 136

Query: 442 VKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           +K  FS+ G VV          ++ +    ++  +VE A  A+  
Sbjct: 137 LKVLFSSNGGVVKGFK----FFQKDRKMALIQMGSVEEAVQALID 177

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 57.2 bits (138), Expect = 1e-09
 Identities = 21/96 (21%), Positives = 35/96 (36%), Gaps = 6/96 (6%)

Query: 219 LIIRNI-PFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           L++ N+ P +     +  +F   G V  V I  N      K  A V+      A+ A+  
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGD 313
            NG K   +PI +  +  +N+              D
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKD 96

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 49.9 bits (119), Expect = 5e-07
 Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 5/81 (6%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
             L + NIP      ++K +FS  G      +         +  A ++     +A  A+ 
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNG----GVVKGFKFFQKDRKMALIQMGSVEEAVQALI 176

Query: 277 KFNGQKFGK-RPIAVDWAVPK 296
             +    G+   + V ++   
Sbjct: 177 DLHNHDLGENHHLRVSFSKST 197

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 44.1 bits (104), Expect = 4e-05
 Identities = 12/58 (20%), Positives = 22/58 (37%)

Query: 9  EHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAE 66
            +    VQ A    A  A+   NG  + G+ I +  + H+     R  +  Q +  +
Sbjct: 39 NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKD 96

>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 Length = 229

 Score = 78.5 bits (193), Expect = 1e-16
 Identities = 38/235 (16%), Positives = 77/235 (32%), Gaps = 56/235 (23%)

Query: 425 QNTIFICNL-PFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAA 483
            + + + NL P  +  + +   F  +G+V         +    K    ++      A  A
Sbjct: 34  NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVK-----ILFNKKENALVQMADGNQAQLA 88

Query: 484 VSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGT 543
           +S        G  L G+ + +  +  + +   +E                       E  
Sbjct: 89  MSHLN-----GHKLHGKPIRITLSKHQNVQLPREGQ---------------------EDQ 122

Query: 544 PAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVV 603
              +   +  + + +    K    +  P+       L + N+P S++E+ LK L      
Sbjct: 123 GLTKDYGNSPLHRFKKPGSKNFQNIFPPS-----ATLHLSNIPPSVSEEDLKVLF----- 172

Query: 604 SRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
              S    V+K  KF Q             R +A ++    + A+ AL  L+N+ 
Sbjct: 173 ---SSNGGVVKGFKFFQK-----------DRKMALIQMGSVEEAVQALIDLHNHD 213

>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 Length = 229

 Score = 57.3 bits (138), Expect = 2e-09
 Identities = 22/100 (22%), Positives = 38/100 (38%), Gaps = 6/100 (6%)

Query: 200 GTVWARQLGGEGSKTQKWKLIIRNI-PFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSK 258
           G+   R      +      L++ N+ P +     +  +F   G V  V I  N      K
Sbjct: 18  GSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KK 72

Query: 259 GFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNI 298
             A V+      A+ A+   NG K   +PI +  +  +N+
Sbjct: 73  ENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNV 112

>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 Length = 229

 Score = 51.5 bits (123), Expect = 2e-07
 Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 5/79 (6%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + NIP      ++K +FS  G V   +     D    +  A ++     +A  A+   
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDL 209

Query: 279 NGQKFG-KRPIAVDWAVPK 296
           +    G    + V ++   
Sbjct: 210 HNHDLGENHHLRVSFSKST 228

>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 Length = 229

 Score = 43.1 bits (101), Expect = 1e-04
 Identities = 12/54 (22%), Positives = 20/54 (37%)

Query: 9   EHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQE 62
             +    VQ A    A  A+   NG  + G+ I +  + H+     R  +  Q 
Sbjct: 70  NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQG 123

>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 Length = 109

 Score = 74.8 bits (184), Expect = 2e-16
 Identities = 27/88 (30%), Positives = 41/88 (46%), Gaps = 4/88 (4%)

Query: 214 TQKWKLIIRNIPFKAKVNEIKDMFSPVG-LVWNVYIPHN-TDTGLSKGFAFVKFTCKRDA 271
           +   +L I  IP   K  EI +  + V   V +V +  +  D   ++GFAFV++   R A
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65

Query: 272 ESAIQKFNGQKF--GKRPIAVDWAVPKN 297
             A +K    +       IAVDWA P+ 
Sbjct: 66  AMARRKLMPGRIQLWGHQIAVDWAEPEI 93

>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 Length = 109

 Score = 62.1 bits (151), Expect = 5e-12
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 5/81 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLH--QVTKRPKGTGFLKFKTVEAATAA 483
             +FI  +P     EE+ +  +   E V  V V        + +G  F+++++  AA  A
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 484 VSASKTTSGLGIFLKGRQLTV 504
               +      I L G Q+ V
Sbjct: 69  R---RKLMPGRIQLWGHQIAV 86

>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 Length = 109

 Score = 47.1 bits (112), Expect = 9e-07
 Identities = 20/88 (22%), Positives = 33/88 (37%), Gaps = 13/88 (14%)

Query: 575 VSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSR 634
               RL I  +PK    + + +          +K    +  +    S        K  +R
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEI--------AKVTEGVLDVIVYASAAD-----KMKNR 52

Query: 635 GVAFVEFTEHQHALVALRVLNNNPSKLF 662
           G AFVE+  H+ A +A R L     +L+
Sbjct: 53  GFAFVEYESHRAAAMARRKLMPGRIQLW 80

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 73.7 bits (182), Expect = 2e-16
 Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            + + N+ + A   ++K++FS  G V+NV + ++ +T   KGF FV+   +     AI K
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAIAK 61

Query: 278 FNGQKFGKRPIAVDWAVPK 296
            +   F  R I V  A PK
Sbjct: 62  LDNTDFMGRTIRVTEANPK 80

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 61.4 bits (150), Expect = 5e-12
 Identities = 27/86 (31%), Positives = 47/86 (54%), Gaps = 8/86 (9%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            I++ NL +   +E+VK+ FS FG+V +   +  + TK+PKG GF++ +  E+ + A++ 
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 487 SKTTSGL-GIFLKGRQLTVLKALDKK 511
                 L      GR + V +A  KK
Sbjct: 62  ------LDNTDFMGRTIRVTEANPKK 81

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 43.7 bits (104), Expect = 7e-06
 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          ++  + + + +GFG+V+    E  + A+   + T   GR I V  A  + SLE    
Sbjct: 33 LIYDRETKKPKGFGFVEMQE-ESVSEAIAKLDNTDFMGRTIRVTEANPKKSLEHHHH 88

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 74.7 bits (184), Expect = 2e-16
 Identities = 29/93 (31%), Positives = 45/93 (48%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           ++  +    +IK  F+P G + +  +  +  TG SKG+ FV F  K DAE+AIQ+  GQ 
Sbjct: 22  DLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW 81

Query: 283 FGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGN 315
            G R I  +WA  K         +  +  G  +
Sbjct: 82  LGGRQIRTNWATRKPPAPKSTYESNTKQSGPSS 114

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 58.5 bits (142), Expect = 1e-10
 Identities = 25/102 (24%), Positives = 40/102 (39%), Gaps = 8/102 (7%)

Query: 410 SKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGT 469
           S     K+          +F+ +L  ++  E++K  F+ FG +     V    T + KG 
Sbjct: 3   SGSSGQKKDTSNH---FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGY 59

Query: 470 GFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           GF+ F     A  A+         G +L GRQ+    A  K 
Sbjct: 60  GFVSFFNKWDAENAIQQMG-----GQWLGGRQIRTNWATRKP 96

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 50.0 bits (120), Expect = 8e-08
 Identities = 13/48 (27%), Positives = 23/48 (47%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
           +G+G+V F    DA  A++   G  +GGR+I    A  +    +   +
Sbjct: 57  KGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYE 104

>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} Length = 88

 Score = 73.7 bits (182), Expect = 2e-16
 Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 1/80 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHN-TDTGLSKGFAFVKFTCKRDAESAIQ 276
           K+ I  +      + I ++FS  G +  + +P       LSKG+A+V+F    +AE A++
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 277 KFNGQKFGKRPIAVDWAVPK 296
             +G +   + I     +  
Sbjct: 66  HMDGGQIDGQEITATAVLAP 85

>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} Length = 88

 Score = 64.1 bits (157), Expect = 5e-13
 Identities = 16/88 (18%), Positives = 37/88 (42%), Gaps = 8/88 (9%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVS-FVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
             + I  L  ++  + + + FS +G++    +PV        KG  +++F+  + A  A+
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 485 SASKTTSGL-GIFLKGRQLTVLKALDKK 511
                   + G  + G+++T    L   
Sbjct: 65  KH------MDGGQIDGQEITATAVLAPW 86

>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} Length = 88

 Score = 50.2 bits (121), Expect = 4e-08
 Identities = 10/50 (20%), Positives = 25/50 (50%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRA 50
           V +   +  +G+ YV+F   ++A +A++  +G  + G++I     +   
Sbjct: 37 PVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPW 86

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 74.0 bits (182), Expect = 2e-16
 Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 6/86 (6%)

Query: 208 GGEGSKTQK---WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVK 264
           G  GS  Q      + +R +P++A  N+I + FSP+  +  V+I    D G   G A V+
Sbjct: 4   GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPD-GRVTGEADVE 61

Query: 265 FTCKRDAESAIQKFNGQKFGKRPIAV 290
           F    DA +A+ K +      R + +
Sbjct: 62  FATHEDAVAAMAK-DKANMQHRYVEL 86

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 48.9 bits (117), Expect = 2e-07
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 8/83 (9%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
            + + +  LP+     ++   FS        V +      R  G   ++F T E A AA+
Sbjct: 15  GHCVHMRGLPYRATENDIYNFFSPLN--PMRVHIEIGPDGRVTGEADVEFATHEDAVAAM 72

Query: 485 SASKTTSGLGIFLKGRQLTVLKA 507
           +  K        ++ R + +   
Sbjct: 73  AKDKA------NMQHRYVELFLN 89

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 1/32 (3%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKI 41
            G   V+FA  EDA  A+  K+  ++  R +
Sbjct: 54 VTGEADVEFATHEDAVAAMA-KDKANMQHRYV 84

>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 Length = 124

 Score = 74.9 bits (184), Expect = 3e-16
 Identities = 23/109 (21%), Positives = 49/109 (44%), Gaps = 6/109 (5%)

Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWN-VYIPHNTDTGLSKGFAFVKFTCKRD 270
                + + ++ +PF+A+   + D F  + +V + +YI +  + G + G  FV+F  + D
Sbjct: 21  PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPN-GKATGEGFVEFRNEAD 79

Query: 271 AESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSG 319
            ++A+ + + Q  G R I V     K +         ++ +      SG
Sbjct: 80  YKAALCR-HKQYMGNRFIQVHPITKKGMLE---KIDMIRKRLQSGPSSG 124

>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 Length = 124

 Score = 63.3 bits (154), Expect = 2e-12
 Identities = 24/122 (19%), Positives = 47/122 (38%), Gaps = 10/122 (8%)

Query: 407 SSKSKPKSLKQTEGED--ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTK 464
           SS   P   K++      E    +++  LPF+ +N+ V   F     V   + + +    
Sbjct: 5   SSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNG 64

Query: 465 RPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNE 524
           +  G GF++F+      AA+   K       ++  R + V     K +   ++ID  +  
Sbjct: 65  KATGEGFVEFRNEADYKAALCRHKQ------YMGNRFIQVHPITKKGM--LEKIDMIRKR 116

Query: 525 TN 526
             
Sbjct: 117 LQ 118

>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 Length = 124

 Score = 41.7 bits (98), Expect = 9e-05
 Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 2   VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           +    + +  G G+V+F    D   A+  ++   +G R I V     +  LE+   
Sbjct: 58  IAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEKIDM 112

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 74.0 bits (182), Expect = 3e-16
 Identities = 22/101 (21%), Positives = 43/101 (42%), Gaps = 3/101 (2%)

Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDA 271
                  + +  +PF A  N+++D F  +  V  V++  +   G + G   VKF   +D 
Sbjct: 12  INPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHV-GRNNGNGLVKFLSPQDT 69

Query: 272 ESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKG 312
             A+++ N     +R + V  A  +   ++GG      + G
Sbjct: 70  FEALKR-NRMLMIQRYVEVSPATERQWVAAGGHITSGPSSG 109

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 52.8 bits (127), Expect = 7e-09
 Identities = 17/102 (16%), Positives = 36/102 (35%), Gaps = 8/102 (7%)

Query: 411 KPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTG 470
              S  +    +     + +  +PF     +V+  F      V  V +L     R  G G
Sbjct: 2   SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR--VDAVHLLKDHVGRNNGNG 59

Query: 471 FLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKL 512
            +KF + +    A+  ++        +  R + V  A +++ 
Sbjct: 60  LVKFLSPQDTFEALKRNRM------LMIQRYVEVSPATERQW 95

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 41.7 bits (98), Expect = 6e-05
 Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 1/37 (2%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          + G G V+F   +D   A++ +N   +  R + V  A
Sbjct: 55 NNGNGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPA 90

>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 Length = 89

 Score = 73.3 bits (181), Expect = 3e-16
 Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           N+ + A   E++  F   G V  V I  +  +G  KGFA+++F+ K    +++   +   
Sbjct: 13  NVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESL 71

Query: 283 FGKRPIAVDWAVPK 296
           F  R I V      
Sbjct: 72  FRGRQIKVIPKRTN 85

>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 Length = 89

 Score = 68.3 bits (168), Expect = 2e-14
 Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 6/88 (6%)

Query: 420 GEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
           G +    +I++ N+ +    EE++  F   G V     +  + +  PKG  +++F   E+
Sbjct: 1   GMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60

Query: 480 ATAAVSASKTTSGLGIFLKGRQLTVLKA 507
              +++            +GRQ+ V+  
Sbjct: 61  VRTSLALD------ESLFRGRQIKVIPK 82

>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 Length = 89

 Score = 45.2 bits (108), Expect = 2e-06
 Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          ++  K S   +GF Y++F+  E    ++ + + +   GR+I V   
Sbjct: 38 ILCDKFSGHPKGFAYIEFSDKESVRTSLAL-DESLFRGRQIKVIPK 82

>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 Length = 109

 Score = 73.5 bits (181), Expect = 4e-16
 Identities = 20/86 (23%), Positives = 40/86 (46%), Gaps = 3/86 (3%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++ + N+P   +  +I+D+F   G + ++ + +         FAFV+F   RDAE A+  
Sbjct: 24  RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG---GPPFAFVEFEDPRDAEDAVYG 80

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGG 303
            +G  +    + V++        SG 
Sbjct: 81  RDGYDYDGYRLRVEFPRSGRGTGSGP 106

>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 Length = 109

 Score = 52.3 bits (126), Expect = 1e-08
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 10/80 (12%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             I++ NLP D+  ++++  F  +G +     +  +  +      F++F+    A  AV 
Sbjct: 23  CRIYVGNLPPDIRTKDIEDVFYKYGAIRD---IDLKNRRGGPPFAFVEFEDPRDAEDAV- 78

Query: 486 ASKTTSGL-GIFLKGRQLTV 504
                 G  G    G +L V
Sbjct: 79  -----YGRDGYDYDGYRLRV 93

>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 Length = 109

 Score = 46.2 bits (110), Expect = 2e-06
 Identities = 12/53 (22%), Positives = 19/53 (35%)

Query: 5   KGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           K       F +V+F    DA  AV  ++G    G ++ V+            S
Sbjct: 55  KNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPS 107

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 73.1 bits (180), Expect = 4e-16
 Identities = 24/91 (26%), Positives = 37/91 (40%), Gaps = 6/91 (6%)

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVG--LVWNVYIPHNTDTGLSKGFAFVKFT 266
           G         +I+RNI     V+ I    SP     V N+ +  +  T  ++GFAFV+ +
Sbjct: 2   GHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS 61

Query: 267 CKRDAESAIQKFNGQKFGK----RPIAVDWA 293
              DA   +Q             + I VD+A
Sbjct: 62  SAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 64.7 bits (158), Expect = 3e-13
 Identities = 12/84 (14%), Positives = 35/84 (41%), Gaps = 3/84 (3%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFG--EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAA 483
           +TI + N+      + +    S +    V +   +  + T++ +G  F++  +   A+  
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 484 VSASKTTSGLGIFLKGRQLTVLKA 507
           +   ++     + + G+ + V  A
Sbjct: 70  LQILQSLHP-PLKIDGKTIGVDFA 92

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 13/51 (25%), Positives = 27/51 (52%), Gaps = 4/51 (7%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGT----SVGGRKIGVKHAM 47
          ++  K + ++RGF +VQ +   DA++ +++         + G+ IGV  A 
Sbjct: 43 LIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAK 93

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 72.5 bits (179), Expect = 4e-16
 Identities = 19/79 (24%), Positives = 38/79 (48%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L + ++        +++ F       + ++  +  TG S+G+ FV FT + DA++A+  
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 278 FNGQKFGKRPIAVDWAVPK 296
             GQ    RP+ ++WA   
Sbjct: 63  MQGQDLNGRPLRINWAAKL 81

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 60.2 bits (147), Expect = 1e-11
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 5/85 (5%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             +F+ +L  ++D+E ++  F  F   +S   +    T   +G GF+ F + + A  A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDK 510
           + +     G  L GR L +  A   
Sbjct: 62  SMQ-----GQDLNGRPLRINWAAKL 81

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 49.4 bits (119), Expect = 6e-08
 Identities = 12/39 (30%), Positives = 20/39 (51%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
          RG+G+V F   +DA  A++   G  + GR + +  A   
Sbjct: 43 RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL 81

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 72.4 bits (178), Expect = 6e-16
 Identities = 18/89 (20%), Positives = 34/89 (38%), Gaps = 7/89 (7%)

Query: 214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAES 273
           +    ++++N+P  +   E+ D+     L              +K  AFV       A++
Sbjct: 3   SGSSGILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQN 55

Query: 274 AIQKFNGQKFGKRPIAVDWAVPKNIYSSG 302
           AIQ F+   F  + + V       +  SG
Sbjct: 56  AIQMFHQYSFRGKDLIVQLQPTDALLCSG 84

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 55.5 bits (134), Expect = 6e-10
 Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 12/79 (15%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           + I + NLP D + +EV      +     +V        R K T F+     E A  A+ 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVD-------RNKRTAFVTLLNGEQAQNAIQ 58

Query: 486 ASKTTSGLGIFLKGRQLTV 504
                S      +G+ L V
Sbjct: 59  MFHQYS-----FRGKDLIV 72

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 10/45 (22%), Positives = 20/45 (44%)

Query: 8  NEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASL 52
          + ++   +V     E A  A++M +  S  G+ + V+     A L
Sbjct: 37 DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDALL 81

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 73.1 bits (180), Expect = 6e-16
 Identities = 23/110 (20%), Positives = 48/110 (43%), Gaps = 7/110 (6%)

Query: 403 SKLNSSKSKPK-SLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQ 461
           S  +S KS  +  +     E+    T+F   L   +   +++  FSA G+V     +  +
Sbjct: 2   SSGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR 61

Query: 462 VTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
            ++R KG  +++F  +++   A+  +      G  L G  + V  +  +K
Sbjct: 62  NSRRSKGIAYVEFCEIQSVPLAIGLT------GQRLLGVPIIVQASQAEK 105

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 70.4 bits (173), Expect = 7e-15
 Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 1/89 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            +    +  + +  +++D FS VG V +V I  + ++  SKG A+V+F   +    AI  
Sbjct: 27  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-G 85

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGGAAA 306
             GQ+    PI V  +  +    SG ++ 
Sbjct: 86  LTGQRLLGVPIIVQASQAEKNRLSGPSSG 114

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           +++ + S   +G  YV+F  ++    A+ +  G  + G  I V+ +    +     S
Sbjct: 57  IISDRNSRRSKGIAYVEFCEIQSVPLAIGL-TGQRLLGVPIIVQASQAEKNRLSGPS 112

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 74.9 bits (184), Expect = 8e-16
 Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 1/89 (1%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           GG        KL++ N+ F     +I+++F+  G +    + ++  +G S G A V F  
Sbjct: 80  GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFER 138

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           + DA  A++++ G     RP+ +     +
Sbjct: 139 RADALKAMKQYKGVPLDGRPMDIQLVASQ 167

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 62.2 bits (151), Expect = 2e-11
 Identities = 21/118 (17%), Positives = 44/118 (37%), Gaps = 12/118 (10%)

Query: 409 KSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKG 468
                S        E    + + NL F + + ++++ F+ FG +     V +  + R  G
Sbjct: 72  HDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKK-AAVDYDRSGRSLG 130

Query: 469 TGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETN 526
           T  + F+    A  A+   K     G+ L GR + +      +L   +   +  +  +
Sbjct: 131 TADVHFERRADALKAMKQYK-----GVPLDGRPMDI------QLVASQIDLEHHHHHH 177

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 49.8 bits (119), Expect = 4e-07
 Identities = 11/47 (23%), Positives = 19/47 (40%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
            G   V F    DA +A++   G  + GR + ++    +  LE    
Sbjct: 129 LGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 175

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 73.2 bits (180), Expect = 9e-16
 Identities = 21/89 (23%), Positives = 40/89 (44%), Gaps = 1/89 (1%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           GG        KL++ N+ F     +I+++F+  G +    +     +G S G A V F  
Sbjct: 27  GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAV-DYDRSGRSLGTADVHFER 85

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           + DA  A++++ G     RP+ +     +
Sbjct: 86  RADALKAMKQYKGVPLDGRPMDIQLVASQ 114

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 64.7 bits (158), Expect = 9e-13
 Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 6/85 (7%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + + NL F + + ++++ F+ FG +     V +  + R  GT  + F+    A  A+ 
Sbjct: 36  AKLLVSNLDFGVSDADIQELFAEFGTLKK-AAVDYDRSGRSLGTADVHFERRADALKAMK 94

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDK 510
             K     G+ L GR + +     +
Sbjct: 95  QYK-----GVPLDGRPMDIQLVASQ 114

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 52.0 bits (125), Expect = 2e-08
 Identities = 11/47 (23%), Positives = 19/47 (40%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
            G   V F    DA +A++   G  + GR + ++    +  LE    
Sbjct: 76  LGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 122

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 71.9 bits (177), Expect = 1e-15
 Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 5/79 (6%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ + N+   A   E++  FS  G +  V+I  N       GFAFV+F   RDAE A++ 
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 278 FNGQKFGKRPIAVDWAVPK 296
            +G+      + V+ +   
Sbjct: 57  LDGKVICGSRVRVELSTGM 75

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 51.1 bits (123), Expect = 3e-08
 Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 10/77 (12%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +++ NL       E+++ FS +G + +       + + P G  F++F+    A  AV   
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTV-----WIARNPPGFAFVEFEDPRDAEDAVRGL 57

Query: 488 KTTSGLGIFLKGRQLTV 504
                 G  + G ++ V
Sbjct: 58  D-----GKVICGSRVRV 69

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 44.2 bits (105), Expect = 7e-06
 Identities = 11/39 (28%), Positives = 19/39 (48%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
           GF +V+F    DA  AV   +G  + G ++ V+ +   
Sbjct: 37 PGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM 75

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 72.3 bits (178), Expect = 1e-15
 Identities = 25/98 (25%), Positives = 38/98 (38%), Gaps = 1/98 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            + + N+ +K    ++K++FS  G+V    I      G S+G   V F    +A  AI  
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAGVVVRADI-LEDKDGKSRGIGTVTFEQSIEAVQAISM 75

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGN 315
           FNGQ    RP+ V                  Q  G  +
Sbjct: 76  FNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSS 113

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 62.7 bits (153), Expect = 3e-12
 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           +T+F+ NL + +  +++K+ FS  G VV    +L     + +G G + F+    A  A+S
Sbjct: 16  STVFVANLDYKVGWKKLKEVFSMAGVVVR-ADILEDKDGKSRGIGTVTFEQSIEAVQAIS 74

Query: 486 ASKTTSGLGIFLKGRQLTV 504
                   G  L  R + V
Sbjct: 75  MFN-----GQLLFDRPMHV 88

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 49.2 bits (118), Expect = 2e-07
 Identities = 14/52 (26%), Positives = 20/52 (38%), Gaps = 3/52 (5%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQE 62
           RG G V F    +A +A+ M NG  +  R + VK          +      E
Sbjct: 56  RGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERA---LPKGDFFPPE 104

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 71.4 bits (176), Expect = 1e-15
 Identities = 14/80 (17%), Positives = 27/80 (33%), Gaps = 2/80 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L IR +       ++  +  P G + +     +  T   KG+ FV F     A+ A+  
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 278 FNGQKFGKRPIAVDWAVPKN 297
                   +      + P +
Sbjct: 67  LKASGVQAQMAKQ--SGPSS 84

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 62.5 bits (153), Expect = 2e-12
 Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           ++I  L     ++++ +    +G++VS   +L + T + KG GF+ F +  AA  AV+A 
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 488 KTTSGLGIFLKGRQLTV 504
           K        ++ +    
Sbjct: 68  K-----ASGVQAQMAKQ 79

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 10/39 (25%), Positives = 18/39 (46%)

Query: 5  KGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
          K +N+ +G+G+V F     A +AV     + V  +    
Sbjct: 41 KTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQ 79

>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} Length = 87

 Score = 71.4 bits (176), Expect = 1e-15
 Identities = 27/69 (39%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 230 VNE--IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRP 287
           +    I   F+P G + +  +  +  TG SKG+ FV F  K DAE+AIQ+  GQ  G R 
Sbjct: 18  ITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ 77

Query: 288 IAVDWAVPK 296
           I  +WA  K
Sbjct: 78  IRTNWATRK 86

>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} Length = 87

 Score = 56.0 bits (136), Expect = 4e-10
 Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 5/83 (6%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +F+ +L  ++    +   F+ FG +     V    T + KG GF+ F     A  A+   
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68

Query: 488 KTTSGLGIFLKGRQLTVLKALDK 510
                 G +L GRQ+    A  K
Sbjct: 69  G-----GQWLGGRQIRTNWATRK 86

>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} Length = 87

 Score = 48.7 bits (117), Expect = 1e-07
 Identities = 13/39 (33%), Positives = 21/39 (53%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
          +G+G+V F    DA  A++   G  +GGR+I    A  +
Sbjct: 48 KGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86

>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 Length = 104

 Score = 71.5 bits (176), Expect = 2e-15
 Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 9/106 (8%)

Query: 208 GGEGSKTQK------WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIP-HNTDTGLSKGF 260
           G  GS   +      +   + N+P+      IK+ F  + +   V +P   ++    KGF
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNIS-AVRLPREPSNPERLKGF 59

Query: 261 AFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAA 306
            + +F       SA+   N +  G + I VD A       SG ++ 
Sbjct: 60  GYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKDSGPSSG 104

>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 Length = 104

 Score = 59.2 bits (144), Expect = 5e-11
 Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 6/85 (7%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T F+ NLP+D+  E +K+ F         +P      +R KG G+ +F+ +++  +A+S 
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76

Query: 487 SKTTSGLGIFLKGRQLTVLKALDKK 511
           +         L  +++ V  A   +
Sbjct: 77  N------EESLGNKRIRVDVADQAQ 95

>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 Length = 104

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           +GFGY +F  ++    A+ + N  S+G ++I V  A      +   S
Sbjct: 57  KGFGYAEFEDLDSLLSALSL-NEESLGNKRIRVDVADQAQDKDSGPS 102

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 71.2 bits (175), Expect = 2e-15
 Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 6/97 (6%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G E + +    L +RN+        I+  F+ +       +         + +AFV F+ 
Sbjct: 7   GDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSN 60

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGA 304
           + DA  A++  NG+     PI V  A P +  SSG +
Sbjct: 61  REDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPS 97

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 11/78 (14%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            +++ NL      E +++ F+             +  K+ +   F+ F   E A  A+ A
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAV------ERVKKIRDYAFVHFSNREDAVEAMKA 70

Query: 487 SKTTSGLGIFLKGRQLTV 504
                  G  L G  + V
Sbjct: 71  LN-----GKVLDGSPIEV 83

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 43.8 bits (104), Expect = 9e-06
 Identities = 14/48 (29%), Positives = 20/48 (41%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           R + +V F+  EDA  A++  NG  + G  I V  A          S
Sbjct: 50 IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPS 97

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 72.1 bits (177), Expect = 2e-15
 Identities = 15/76 (19%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           + N+ + +   +++  FS  G +  + I  +  +G  KG+A+++F  +   ++A+   + 
Sbjct: 41  VGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDE 99

Query: 281 QKFGKRPIAVDWAVPK 296
             F  R I V      
Sbjct: 100 TVFRGRTIKVLPKRTN 115

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 71.7 bits (176), Expect = 3e-15
 Identities = 20/115 (17%), Positives = 51/115 (44%), Gaps = 6/115 (5%)

Query: 397 AKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFV 456
              S ++    ++  P+ L   E ++  + ++++ N+ +    ++++  FS+ G +    
Sbjct: 8   TTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRIT 67

Query: 457 PVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
            +  + +  PKG  +++F    +  AAV+  +T        +GR + VL      
Sbjct: 68  ILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETV------FRGRTIKVLPKRTNM 116

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 41.2 bits (97), Expect = 1e-04
 Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 1/36 (2%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           +G+ Y++FA     + AV M + T   GR I V   
Sbjct: 78  KGYAYIEFAERNSVDAAVAM-DETVFRGRTIKVLPK 112

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 71.2 bits (175), Expect = 2e-15
 Identities = 26/105 (24%), Positives = 44/105 (41%), Gaps = 11/105 (10%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVG-LVWNVYIPHNTDTGLSKGFAFVKFT 266
           G  GS      L + ++      N I   F+ +G  V +V I  N  TG+  G+ FV+F 
Sbjct: 1   GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60

Query: 267 CKRDAESAIQKFNGQKFG----KRPIAVDWAVPKNIYSSGGAAAG 307
               AE  + K NG+        +   +++A      +  G ++G
Sbjct: 61  DLATAEKCLHKINGKPLPGATPAKRFKLNYA------TYSGPSSG 99

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 53.9 bits (130), Expect = 3e-09
 Identities = 14/68 (20%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 420 GEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLH-QVTKRPKGTGFLKFKTVE 478
           G   +  ++++ +L   +D   + + F+  GE V  V ++  ++T  P G  F++F  + 
Sbjct: 4   GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLA 63

Query: 479 AATAAVSA 486
            A   +  
Sbjct: 64  TAEKCLHK 71

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 8/43 (18%), Positives = 19/43 (44%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
          ++  + +    G+ +V+FA +  A + +   NG  + G     
Sbjct: 42 IIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK 84

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 71.2 bits (175), Expect = 3e-15
 Identities = 31/104 (29%), Positives = 48/104 (46%), Gaps = 2/104 (1%)

Query: 193 HQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNT 252
           H      G V         +K+Q  +L + NIPF+ +  +++ MF   G + +V I    
Sbjct: 6   HHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII--F 63

Query: 253 DTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           +   SKGF FV F    DA+ A +K +G     R I V+ A  +
Sbjct: 64  NERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 59.6 bits (145), Expect = 3e-11
 Identities = 22/104 (21%), Positives = 44/104 (42%), Gaps = 7/104 (6%)

Query: 407 SSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRP 466
           SS   P+              + + N+PF   + +++Q F  FG+++    + ++  +  
Sbjct: 11  SSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGS 68

Query: 467 KGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
           KG GF+ F+    A  A          G  ++GR++ V  A  +
Sbjct: 69  KGFGFVTFENSADADRAREKLH-----GTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 20/39 (51%), Positives = 25/39 (64%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
           +GFG+V F    DA+RA E  +GT V GRKI V +A  R
Sbjct: 69  KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 71.1 bits (175), Expect = 3e-15
 Identities = 24/93 (25%), Positives = 40/93 (43%), Gaps = 6/93 (6%)

Query: 212 SKTQKWKLIIRNIPFKAKVNE--IKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKR 269
              Q   L + N+     V E  I  +FS +G   +  +     +     + FV+F   R
Sbjct: 11  DDGQPRTLYVGNLSRD--VTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHR 66

Query: 270 DAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSG 302
           DA +A+   NG+K   + + V+WA   +   SG
Sbjct: 67  DAAAALAAMNGRKILGKEVKVNWATTPSSQKSG 99

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 10/98 (10%)

Query: 417 QTEGEDELQN-TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFK 475
               ED+ Q  T+++ NL  D+    + Q FS  G   S   +    +  P    F++F 
Sbjct: 6   SGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFY 63

Query: 476 TVEAATAAVSASKTTSGL-GIFLKGRQLTVLKALDKKL 512
               A AA++A      + G  + G+++ V  A     
Sbjct: 64  EHRDAAAALAA------MNGRKILGKEVKVNWATTPSS 95

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 3/48 (6%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          +  + +V+F    DA  A+   NG  + G+++ V  A        ++S
Sbjct: 54 NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTP---SSQKS 98

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 70.8 bits (174), Expect = 3e-15
 Identities = 15/71 (21%), Positives = 23/71 (32%), Gaps = 6/71 (8%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           NIP  A   ++  +F   G + +            KG  F+K+     A   I       
Sbjct: 34  NIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVALANFP 87

Query: 283 FGKRPIAVDWA 293
           F  R +   W 
Sbjct: 88  FQGRNLRTGWG 98

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 55.4 bits (134), Expect = 7e-10
 Identities = 20/95 (21%), Positives = 34/95 (35%), Gaps = 12/95 (12%)

Query: 411 KPKSLKQTEGEDELQNT-IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGT 469
            P+++         + T  +I N+P      ++   F  FG ++ F           KG 
Sbjct: 12  NPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDF------KHYPEKGC 65

Query: 470 GFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV 504
            F+K+ T E A   + A           +GR L  
Sbjct: 66  CFIKYDTHEQAAVCIVALA-----NFPFQGRNLRT 95

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 41.9 bits (99), Expect = 5e-05
 Identities = 5/32 (15%), Positives = 12/32 (37%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKI 41
           +G  ++++   E A   +         GR +
Sbjct: 62 EKGCCFIKYDTHEQAAVCIVALANFPFQGRNL 93

>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 Length = 90

 Score = 70.3 bits (173), Expect = 3e-15
 Identities = 13/84 (15%), Positives = 31/84 (36%), Gaps = 2/84 (2%)

Query: 216 KWKLIIRNIPFKAKVNEIKDMFSPVGL--VWNVYIPHNTDTGLSKGFAFVKFTCKRDAES 273
           +  L I N+ +     ++ +    +G+  +  +    N   G SKGFA V    +  ++ 
Sbjct: 1   RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60

Query: 274 AIQKFNGQKFGKRPIAVDWAVPKN 297
            +     ++   +   V  +    
Sbjct: 61  LMDLLPKRELHGQNPVVTPSNKLE 84

>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 Length = 90

 Score = 56.4 bits (137), Expect = 2e-10
 Identities = 11/86 (12%), Positives = 33/86 (38%), Gaps = 9/86 (10%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFG--EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATA 482
           +  ++I NL +   +E++ +   + G  +++      ++   + KG   +   +  ++  
Sbjct: 1   RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60

Query: 483 AVSASKTTSGL-GIFLKGRQLTVLKA 507
            +        L    L G+   V  +
Sbjct: 61  LMDL------LPKRELHGQNPVVTPS 80

>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 Length = 90

 Score = 46.0 bits (110), Expect = 1e-06
 Identities = 6/48 (12%), Positives = 15/48 (31%), Gaps = 3/48 (6%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
          +GF  V       + + +++     + G+   V  +      E     
Sbjct: 45 KGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKL---EHHHHH 89

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 70.3 bits (173), Expect = 3e-15
 Identities = 22/94 (23%), Positives = 35/94 (37%), Gaps = 8/94 (8%)

Query: 211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRD 270
            S     KL + NI       E++  F   G V    I         K +AFV      D
Sbjct: 5   SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAED 56

Query: 271 AESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGA 304
           A  AI+  +  +F  + + V  +  +   +SG +
Sbjct: 57  AVEAIRGLDNTEFQGKRMHVQLSTSRLRTASGPS 90

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 14/83 (16%), Positives = 31/83 (37%), Gaps = 15/83 (18%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + + N+     N+E++ +F  +G V+             K   F+  +  E A  A+ 
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIE--------CDIVKDYAFVHMERAEDAVEAIR 62

Query: 486 ASKTTSGL-GIFLKGRQLTVLKA 507
                  L     +G+++ V  +
Sbjct: 63  G------LDNTEFQGKRMHVQLS 79

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 10/47 (21%), Positives = 20/47 (42%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          + + +V     EDA  A+   + T   G+++ V+ +  R       S
Sbjct: 44 KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTASGPS 90

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 70.8 bits (174), Expect = 3e-15
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 8/81 (9%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLV--------WNVYIPHNTDTGLSKGFAFVKFTCKRDAE 272
           ++ +     +  + D F  +G++          + +  + +TG  KG A V F     A+
Sbjct: 18  VQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAK 77

Query: 273 SAIQKFNGQKFGKRPIAVDWA 293
           +AI  F+G++F   PI V +A
Sbjct: 78  AAIDWFDGKEFSGNPIKVSFA 98

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 58.5 bits (142), Expect = 7e-11
 Identities = 20/91 (21%), Positives = 31/91 (34%), Gaps = 15/91 (16%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQV--------TKRPKGTGFLKFKTV 477
           NTIF+  L  ++  E V   F   G + +       +        T + KG   + F   
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 478 EAATAAVSASKTTSGL-GIFLKGRQLTVLKA 507
            +A AA+          G    G  + V  A
Sbjct: 74  PSAKAAIDW------FDGKEFSGNPIKVSFA 98

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 11/46 (23%), Positives = 19/46 (41%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          + T + + + +G   V F     A  A++  +G    G  I V  A
Sbjct: 53 LYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>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 Length = 172

 Score = 73.0 bits (180), Expect = 3e-15
 Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 5/82 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           + +FI  LP  L++++VK+  ++FG + +F  V    T   KG  F ++  +     A++
Sbjct: 95  HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154

Query: 486 ASKTTSGLGIFLKGRQLTVLKA 507
                   G+ L  ++L V +A
Sbjct: 155 GLN-----GMQLGDKKLLVQRA 171

>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 Length = 172

 Score = 69.6 bits (171), Expect = 4e-14
 Identities = 36/235 (15%), Positives = 67/235 (28%), Gaps = 87/235 (37%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFV-----PVLHQVTKRPKGTGFLKFKTVEAAT 481
            +++ N+PF +  E +   F+A   +         PVL     + K   FL+F++V+  T
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 482 AAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILE 541
            A++        GI  +G+ L + +                        L+         
Sbjct: 66  QAMAFD------GIIFQGQSLKIRRP------------HDYQPLPGAHKLF--------- 98

Query: 542 GTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDA 601
                                                   I  LP  + +  +K+L    
Sbjct: 99  ----------------------------------------IGGLPNYLNDDQVKELL--- 115

Query: 602 VVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNN 656
                      +K    ++    G       S+G AF E+ +      A+  LN 
Sbjct: 116 ------TSFGPLKAFNLVKDSATGL------SKGYAFCEYVDINVTDQAIAGLNG 158

>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 Length = 172

 Score = 67.6 bits (166), Expect = 2e-13
 Identities = 24/110 (21%), Positives = 48/110 (43%), Gaps = 1/110 (0%)

Query: 185 ACASVAL-LHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLV 243
              + A+       +G ++  R+           KL I  +P     +++K++ +  G +
Sbjct: 62  DETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPL 121

Query: 244 WNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA 293
               +  ++ TGLSKG+AF ++      + AI   NG + G + + V  A
Sbjct: 122 KAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>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 Length = 172

 Score = 60.7 bits (148), Expect = 6e-11
 Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 6/85 (7%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIP-----HNTDTGLSKGFAFVKFTCKRDAE 272
           +L + NIPF      + D F+    +  +                K FAF++F    +  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 273 SAIQKFNGQKFGKRPIAVDWAVPKN 297
            A+  F+G  F  + + +       
Sbjct: 66  QAM-AFDGIIFQGQSLKIRRPHDYQ 89

>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 Length = 172

 Score = 50.7 bits (122), Expect = 2e-07
 Identities = 9/46 (19%), Positives = 24/46 (52%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           +V    +   +G+ + ++  +   ++A+   NG  +G +K+ V+ A
Sbjct: 126 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>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 Length = 172

 Score = 46.1 bits (110), Expect = 6e-06
 Identities = 7/45 (15%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          V     N+ + F +++F  +++  +A+   +G    G+ + ++  
Sbjct: 42 VLAVQINQDKNFAFLEFRSVDETTQAMAF-DGIIFQGQSLKIRRP 85

>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 Length = 107

 Score = 70.8 bits (174), Expect = 4e-15
 Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           GG        KL++ N+ F     +I+++F+  G +    + H   +G S G A V F  
Sbjct: 21  GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAV-HYDRSGRSLGTADVHFER 79

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAV 294
           K DA  A++++NG     RP+ +    
Sbjct: 80  KADALKAMKQYNGVPLDGRPMNIQLVT 106

>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 Length = 107

 Score = 61.1 bits (149), Expect = 9e-12
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 6/79 (7%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + + NL F + + ++++ F+ FG +     V +  + R  GT  + F+    A  A+ 
Sbjct: 30  GKLLVSNLDFGVSDADIQELFAEFGTLKK-AAVHYDRSGRSLGTADVHFERKADALKAMK 88

Query: 486 ASKTTSGLGIFLKGRQLTV 504
                   G+ L GR + +
Sbjct: 89  QYN-----GVPLDGRPMNI 102

>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 Length = 107

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 10/36 (27%), Positives = 17/36 (47%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
            G   V F    DA +A++  NG  + GR + ++  
Sbjct: 70  LGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 105

>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 Length = 229

 Score = 74.4 bits (182), Expect = 4e-15
 Identities = 14/115 (12%), Positives = 38/115 (33%), Gaps = 2/115 (1%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGL--VWNVYIPHNTDTGLSKGFAFVKF 265
                  ++  L I N+ +     ++ +    +G+  +  +    N   G SKGFA V  
Sbjct: 60  VVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGV 119

Query: 266 TCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGS 320
             +  ++  +     ++   +   V     + +      +      G  + +  +
Sbjct: 120 GSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKA 174

>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 Length = 229

 Score = 67.4 bits (164), Expect = 1e-12
 Identities = 18/159 (11%), Positives = 49/159 (30%), Gaps = 10/159 (6%)

Query: 374 LSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNL 433
           L DD      N     +           V       + P  +    G+   +  ++I NL
Sbjct: 20  LYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGK---RIALYIGNL 76

Query: 434 PFDLDNEEVKQRFSAFG--EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTS 491
            +   +E++ +   + G  +++      ++   + KG   +   +  ++   +       
Sbjct: 77  TWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLP--- 133

Query: 492 GLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRN 530
                L G+   V     + L+  +   +   ++     
Sbjct: 134 --KRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSG 170

>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 Length = 229

 Score = 47.8 bits (113), Expect = 4e-06
 Identities = 5/55 (9%), Positives = 18/55 (32%)

Query: 2   VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRR 56
              + + + +GF  V       + + +++     + G+   V     +   +   
Sbjct: 103 FENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEM 157

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 70.7 bits (174), Expect = 4e-15
 Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 2/80 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            + I+N+        + D FS  G + +  +    D   SKG+ FV F  +  AE AI+K
Sbjct: 7   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQEAAERAIEK 64

Query: 278 FNGQKFGKRPIAVDWAVPKN 297
            NG     R + V     + 
Sbjct: 65  MNGMLLNDRKVFVGRFKSRK 84

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 65.3 bits (160), Expect = 4e-13
 Identities = 32/101 (31%), Positives = 49/101 (48%), Gaps = 7/101 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             IFI NL   +DN+ +   FSAFG ++S   V+       KG GF+ F+T EAA  A+ 
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILS-CKVVCD-ENGSKGYGFVHFETQEAAERAIE 63

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETN 526
                   G+ L  R++ V +   +K    +   ++K  TN
Sbjct: 64  KMN-----GMLLNDRKVFVGRFKSRKEREAELGARAKEFTN 99

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 51.9 bits (125), Expect = 2e-08
 Identities = 18/55 (32%), Positives = 25/55 (45%)

Query: 8  NEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQE 62
          N  +G+G+V F   E A RA+E  NG  +  RK+ V     R   E       +E
Sbjct: 42 NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKE 96

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 69.9 bits (172), Expect = 4e-15
 Identities = 30/97 (30%), Positives = 41/97 (42%), Gaps = 9/97 (9%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G  GS     KL I N+P +A   EI+ +F   G V    I         K + FV    
Sbjct: 1   GSSGSSGMV-KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIED 51

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGA 304
           K  AE AI+  +  K     I V+ +  K+  SSG +
Sbjct: 52  KTAAEDAIRNLHHYKLHGVNINVEASKNKSKASSGPS 88

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 15/81 (18%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +FI NLP +   +E++  F  +G+V+             K  GF+  +   AA  A+   
Sbjct: 11  LFIGNLPREATEQEIRSLFEQYGKVLEC--------DIIKNYGFVHIEDKTAAEDAIRN- 61

Query: 488 KTTSGL-GIFLKGRQLTVLKA 507
                L    L G  + V  +
Sbjct: 62  -----LHHYKLHGVNINVEAS 77

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 8/47 (17%), Positives = 19/47 (40%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          + +G+V       A  A+   +   + G  I V+ + +++      S
Sbjct: 42 KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASSGPS 88

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 70.3 bits (173), Expect = 5e-15
 Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDA 271
           ++ Q   L ++N+        ++  FSP G + +  +    + G SKGF FV F+   +A
Sbjct: 11  TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEEA 68

Query: 272 ESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGA 304
             A+ + NG+    +P+ V  A  K    SG +
Sbjct: 69  TKAVTEMNGRIVATKPLYVALAQRKEERQSGPS 101

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 29/107 (27%), Positives = 47/107 (43%), Gaps = 18/107 (16%)

Query: 407 SSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQV---T 463
           SS S    + + +        +++ NL   +D+E +++ FS FG + S      +V    
Sbjct: 2   SSGSSGDRITRYQV-----VNLYVKNLDDGIDDERLRKAFSPFGTITS-----AKVMMEG 51

Query: 464 KRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
            R KG GF+ F + E AT AV+        G  +  + L V  A  K
Sbjct: 52  GRSKGFGFVCFSSPEEATKAVTEMN-----GRIVATKPLYVALAQRK 93

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 3/47 (6%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          +GFG+V F+  E+A +AV   NG  V  + + V  A  +   E+R+S
Sbjct: 55 KGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRK---EERQS 98

>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 Length = 114

 Score = 70.5 bits (173), Expect = 6e-15
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 3/88 (3%)

Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWN-VYIPHNTDTGLSKGFAFVKFTCKRD 270
             + K    I NIPF     ++      + +  N V++  + + G   G A V+F  + D
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD-NNGQGLGQALVQFKNEDD 69

Query: 271 AESAIQKFNGQKFGKRPIAVDWAVPKNI 298
           A  + +  + +K   R   V     +++
Sbjct: 70  ARKSERL-HRKKLNGREAFVHVVTLEDM 96

>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 Length = 114

 Score = 60.9 bits (148), Expect = 1e-11
 Identities = 18/96 (18%), Positives = 32/96 (33%), Gaps = 7/96 (7%)

Query: 412 PKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGF 471
             S  + +     +    I N+PF +   +V Q         + V VL     +  G   
Sbjct: 3   SGSSGEGDVNSA-KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61

Query: 472 LKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
           ++FK  + A  +    +        L GR+  V   
Sbjct: 62  VQFKNEDDARKSERLHRKK------LNGREAFVHVV 91

>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 Length = 114

 Score = 42.4 bits (100), Expect = 4e-05
 Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 5/48 (10%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
            G   VQF   +DA ++    +   + GR+  V    H  +LE  R 
Sbjct: 56 GLGQALVQFKNEDDARKSER-LHRKKLNGREAFV----HVVTLEDMRE 98

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 73.5 bits (181), Expect = 6e-15
 Identities = 30/124 (24%), Positives = 51/124 (41%), Gaps = 6/124 (4%)

Query: 177 VLYTTVKSACASVALLHQKEIKGGTV---WARQLGGEGSKTQKWKLIIRNIPFKAKVNEI 233
           V +     A  ++  ++   IKG  V   W+++      K+    + I+N+        +
Sbjct: 62  VNFQQPADAERALDTMNFDVIKGKPVRIMWSQR-DPSLRKSGVGNIFIKNLDKSIDNKAL 120

Query: 234 KDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA 293
            D FS  G + +  +    D   SKG+ FV F  +  AE AI+K NG     R + V   
Sbjct: 121 YDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 178

Query: 294 VPKN 297
             + 
Sbjct: 179 KSRK 182

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 73.5 bits (181), Expect = 6e-15
 Identities = 18/75 (24%), Positives = 35/75 (46%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + ++        + + FSP G + ++ +  +  T  S G+A+V F    DAE A+   
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77

Query: 279 NGQKFGKRPIAVDWA 293
           N      +P+ + W+
Sbjct: 78  NFDVIKGKPVRIMWS 92

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 69.2 bits (170), Expect = 2e-13
 Identities = 37/137 (27%), Positives = 58/137 (42%), Gaps = 13/137 (9%)

Query: 404 KLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVT 463
           ++  S+  P   K   G       IFI NL   +DN+ +   FSAFG ++S   V+    
Sbjct: 88  RIMWSQRDPSLRKSGVG------NIFIKNLDKSIDNKALYDTFSAFGNILS-CKVVCD-E 139

Query: 464 KRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKN 523
              KG GF+ F+T EAA  A+         G+ L  R++ V +   +K    +   ++K 
Sbjct: 140 NGSKGYGFVHFETQEAAERAIEKMN-----GMLLNDRKVFVGRFKSRKEREAELGARAKE 194

Query: 524 ETNDHRNLYLAKEGLIL 540
                   Y    G I+
Sbjct: 195 FYPYDVPDYAGSSGRIV 211

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 53.4 bits (129), Expect = 4e-08
 Identities = 19/64 (29%), Positives = 27/64 (42%)

Query: 7   SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAE 66
            N  +G+G+V F   E A RA+E  NG  +  RK+ V     R   E       +E    
Sbjct: 139 ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPY 198

Query: 67  DIEK 70
           D+  
Sbjct: 199 DVPD 202

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 53.1 bits (128), Expect = 4e-08
 Identities = 34/245 (13%), Positives = 66/245 (26%), Gaps = 81/245 (33%)

Query: 412 PKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGF 471
           P              ++++ +L  D+    + ++FS  G ++S       +T+R  G  +
Sbjct: 2   PLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAY 61

Query: 472 LKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNL 531
           + F+    A  A+            +KG+ + ++ +                  +   N+
Sbjct: 62  VNFQQPADAERALDTMN-----FDVIKGKPVRIMWSQRDP----------SLRKSGVGNI 106

Query: 532 YLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTE 591
           +                                                 I NL KS+  
Sbjct: 107 F-------------------------------------------------IKNLDKSIDN 117

Query: 592 KGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVAL 651
           K L                  I   K +        D    S+G  FV F   + A  A+
Sbjct: 118 KALYD---------TFSAFGNILSCKVV-------CDENG-SKGYGFVHFETQEAAERAI 160

Query: 652 RVLNN 656
             +N 
Sbjct: 161 EKMNG 165

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 46.1 bits (110), Expect = 1e-05
 Identities = 10/41 (24%), Positives = 18/41 (43%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKI 41
          +     +    G+ YV F    DA RA++  N   + G+ +
Sbjct: 47 VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 87

>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 Length = 126

 Score = 70.7 bits (173), Expect = 6e-15
 Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 1/82 (1%)

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
                     + +R +PF     EI   FS + +V N         G   G AFV+F  +
Sbjct: 35  NSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQ 94

Query: 269 RDAESAIQKFNGQKFGKRPIAV 290
             AE A+ K + ++ G R I V
Sbjct: 95  ELAEKALGK-HKERIGHRYIEV 115

>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 Length = 126

 Score = 62.2 bits (151), Expect = 6e-12
 Identities = 19/103 (18%), Positives = 37/103 (35%), Gaps = 6/103 (5%)

Query: 405 LNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTK 464
            + +  +         +      + +  LPF    EE+ Q FS    V + + +      
Sbjct: 22  ASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEG 81

Query: 465 RPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
           +  G  F++F + E A  A+   K        +  R + V K+
Sbjct: 82  KITGEAFVQFASQELAEKALGKHKE------RIGHRYIEVFKS 118

>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 Length = 126

 Score = 40.6 bits (95), Expect = 2e-04
 Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 1/37 (2%)

Query: 10  HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
             G  +VQFA  E A +A+  K+   +G R I V  +
Sbjct: 83  ITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKS 118

>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 Length = 150

 Score = 71.4 bits (175), Expect = 7e-15
 Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 5/79 (6%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ + N+       E++  F   G + +V++  N       GFAFV+F   RDA  A+++
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRE 129

Query: 278 FNGQKFGKRPIAVDWAVPK 296
            +G+      + V+ +  +
Sbjct: 130 LDGRTLCGCRVRVELSNGE 148

>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 Length = 150

 Score = 47.2 bits (112), Expect = 2e-06
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 12/86 (13%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            +++ NL  + +  E+++ F  +G + S       V + P G  F++F+    A  AV  
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSV-----WVARNPPGFAFVEFEDPRDAADAV-- 127

Query: 487 SKTTSGL-GIFLKGRQLTVLKALDKK 511
                 L G  L G ++ V  +  +K
Sbjct: 128 ----RELDGRTLCGCRVRVELSNGEK 149

>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 Length = 150

 Score = 46.4 bits (110), Expect = 4e-06
 Identities = 11/42 (26%), Positives = 20/42 (47%)

Query: 8   NEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
               GF +V+F    DA  AV   +G ++ G ++ V+ +   
Sbjct: 107 RNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE 148

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 69.6 bits (171), Expect = 8e-15
 Identities = 20/82 (24%), Positives = 31/82 (37%), Gaps = 3/82 (3%)

Query: 213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTD-TGLSKGFAFVKFTCKRDA 271
           +     + + N+  + +   + ++F   G +  V I    D  G  K F FV F      
Sbjct: 13  EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTIC--KDREGKPKSFGFVCFKHPESV 70

Query: 272 ESAIQKFNGQKFGKRPIAVDWA 293
             AI   NG +   RPI V   
Sbjct: 71  SYAIALLNGIRLYGRPINVSGP 92

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 61.1 bits (149), Expect = 7e-12
 Identities = 24/90 (26%), Positives = 40/90 (44%), Gaps = 8/90 (8%)

Query: 419 EGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVE 478
             ++E   T+F+ NL   +  E + + F   G +   V +      +PK  GF+ FK  E
Sbjct: 10  PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTK-VTICKDREGKPKSFGFVCFKHPE 68

Query: 479 AATAAVSASKTTSGL-GIFLKGRQLTVLKA 507
           + + A++       L GI L GR + V   
Sbjct: 69  SVSYAIAL------LNGIRLYGRPINVSGP 92

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 47.2 bits (113), Expect = 4e-07
 Identities = 12/37 (32%), Positives = 18/37 (48%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           + FG+V F   E  + A+ + NG  + GR I V   
Sbjct: 56 PKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP 92

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 69.6 bits (171), Expect = 1e-14
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 8/92 (8%)

Query: 205 RQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVK 264
                +  +    +L +R  P   + +E+ ++F P G +  V I          GFAFV+
Sbjct: 20  HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVE 71

Query: 265 FTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           F     A  AI++ +G+ F  +P+ V ++   
Sbjct: 72  FEEAESAAKAIEEVHGKSFANQPLEVVYSKLP 103

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 55.4 bits (134), Expect = 1e-09
 Identities = 26/108 (24%), Positives = 42/108 (38%), Gaps = 17/108 (15%)

Query: 407 SSKSKPK-SLKQTEGEDELQNT-IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTK 464
           SS   P+ S      E EL NT +F+   P D+   E+ + F  FG +           K
Sbjct: 11  SSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE--------VK 62

Query: 465 RPKGTGFLKFKTVEAATAAVSASKTTSGL-GIFLKGRQLTVLKALDKK 511
              G  F++F+  E+A  A+        + G     + L V+ +    
Sbjct: 63  ILNGFAFVEFEEAESAAKAIEE------VHGKSFANQPLEVVYSKLPA 104

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 47.3 bits (113), Expect = 8e-07
 Identities = 12/46 (26%), Positives = 24/46 (52%), Gaps = 2/46 (4%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRR 56
            GF +V+F   E A +A+E  +G S   + + V ++  +   ++ R
Sbjct: 65  NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS--KLPAKRYR 108

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 69.2 bits (170), Expect = 1e-14
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
           N+PF     +I  +F  +  + +V +  + DT   KGF +V+F      + A+  ++G  
Sbjct: 22  NLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGAL 79

Query: 283 FGKRPIAVDWAVPKNIYSSGGAA 305
            G R + VD A  +    SG ++
Sbjct: 80  LGDRSLRVDIAEGRKQDKSGPSS 102

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 63.1 bits (154), Expect = 2e-12
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 7/86 (8%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
            T ++ NLPF+    ++   F     + S   V  + T + KG  +++F  V++   A++
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKK 511
                   G  L  R L V  A  +K
Sbjct: 75  YD------GALLGDRSLRVDIAEGRK 94

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 47.3 bits (113), Expect = 5e-07
 Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           +V  K +++ +GF YV+F  ++    A+   +G  +G R + V  A  R   +   S
Sbjct: 46  LVRDKDTDKFKGFCYVEFDEVDSLKEALTY-DGALLGDRSLRVDIAEGRKQDKSGPS 101

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 68.8 bits (169), Expect = 1e-14
 Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 8/89 (8%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G  GS    WK+ + N+       E++ +F   G V    +         K +AFV    
Sbjct: 1   GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEK 52

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           + DA++AI + NG++   + I V+ +   
Sbjct: 53  EADAKAAIAQLNGKEVKGKRINVELSTKG 81

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 46.8 bits (112), Expect = 6e-07
 Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 15/82 (18%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            IF+ N+     ++E++  F   G V+             K   F+  +    A AA++ 
Sbjct: 11  KIFVGNVSAACTSQELRSLFERRGRVIE--------CDVVKDYAFVHMEKEADAKAAIAQ 62

Query: 487 SKTTSGL-GIFLKGRQLTVLKA 507
                 L G  +KG+++ V  +
Sbjct: 63  ------LNGKEVKGKRINVELS 78

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 44.1 bits (105), Expect = 6e-06
 Identities = 10/39 (25%), Positives = 18/39 (46%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
          + + +V      DA  A+   NG  V G++I V+ +   
Sbjct: 43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG 81

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 70.7 bits (173), Expect = 2e-14
 Identities = 16/104 (15%), Positives = 37/104 (35%), Gaps = 2/104 (1%)

Query: 204 ARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGL--VWNVYIPHNTDTGLSKGFA 261
           A      G + ++  + + +  +     ++  +   +G+  V  +    N   G SKG+A
Sbjct: 43  AILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYA 102

Query: 262 FVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAA 305
            V    +      ++   G+      + V  A  +N+      A
Sbjct: 103 EVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQA 146

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 63.8 bits (155), Expect = 4e-12
 Identities = 18/130 (13%), Positives = 41/130 (31%), Gaps = 10/130 (7%)

Query: 383 GNKEQDSDKTVNESAKVSDVSKLNSSK---SKPKSLKQTEGEDELQNTIFICNLPFDLDN 439
           G      +           V +  S K     P  L    G    +  +++ +  +   +
Sbjct: 10  GVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTD 69

Query: 440 EEVKQRFSAFG--EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL 497
           +++ Q   + G  +VV      ++   + KG   +   +  +    +         G  L
Sbjct: 70  QQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLP-----GKVL 124

Query: 498 KGRQLTVLKA 507
            G ++ V  A
Sbjct: 125 NGEKVDVRPA 134

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 48.4 bits (115), Expect = 7e-07
 Identities = 9/49 (18%), Positives = 22/49 (44%)

Query: 2   VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRA 50
              + + + +G+  V  A     ++ +E+  G  + G K+ V+ A  + 
Sbjct: 90  AENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQN 138

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 68.6 bits (168), Expect = 2e-14
 Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDA 271
            + +  KL IRNIP   +   +  +    G+V +     NTD+        V ++ K  A
Sbjct: 11  KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQ-VNTDS--ETAVVNVTYSSKDQA 67

Query: 272 ESAIQKFNGQKFGKRPIAVDWAVPK 296
             A+ K NG +     + V +   +
Sbjct: 68  RQALDKLNGFQLENFTLKVAYIPDE 92

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 54.8 bits (132), Expect = 1e-09
 Identities = 19/89 (21%), Positives = 30/89 (33%), Gaps = 10/89 (11%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + I N+P  L  E +      +G V S   V    T        + + + + A  A+ 
Sbjct: 16  RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV---NTDSETAVVNVTYSSKDQARQALD 72

Query: 486 ASKTTSGL-GIFLKGRQLTVLKALDKKLA 513
                  L G  L+   L V    D+  A
Sbjct: 73  K------LNGFQLENFTLKVAYIPDEMAA 95

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 39.0 bits (91), Expect = 4e-04
 Identities = 6/52 (11%), Positives = 20/52 (38%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLE 53
            +  ++       V ++  + A +A++  NG  +    + V +     + +
Sbjct: 45 CEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 68.4 bits (168), Expect = 2e-14
 Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVY-IPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
            + I N+  +     + D FS  G++     I  + DTG SKG+AF+ F     +++AI+
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 277 KFNGQKFGKRPIAVDWAVPKNIYSSGGA 304
             NGQ    RPI V +A  K+   SG +
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSKGSGPS 94

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 27/86 (31%), Positives = 42/86 (48%), Gaps = 6/86 (6%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVL-HQVTKRPKGTGFLKFKTVEAATAAVS 485
            IFI NL  ++D + +   FSAFG ++    ++    T   KG  F+ F + +A+ AA+ 
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKK 511
           A       G +L  R +TV  A  K 
Sbjct: 67  AMN-----GQYLCNRPITVSYAFKKD 87

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 12/45 (26%), Positives = 24/45 (53%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRAS 51
          +   +G+ ++ FA  + ++ A+E  NG  +  R I V +A  + S
Sbjct: 44 TGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDS 88

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 68.4 bits (168), Expect = 2e-14
 Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 3/92 (3%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTG---LSKGFAFVKFTCKRDAESA 274
            L I+N+ F      +K +FS VG + +  I    +     LS GF FV++     A+ A
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 275 IQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAA 306
           +++  G       + V  +      +SG ++ 
Sbjct: 67  LKQLQGHTVDGHKLEVRISERATKPASGPSSG 98

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 60.7 bits (148), Expect = 9e-12
 Identities = 22/95 (23%), Positives = 37/95 (38%), Gaps = 14/95 (14%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTK---RPKGTGFLKFKTVEAATA 482
           + +FI NL F    E +K  FS  G + S      +         G GF+++K  E A  
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 483 AVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKE 517
           A+   +     G  + G +L V      +++    
Sbjct: 66  ALKQLQ-----GHTVDGHKLEV------RISERAT 89

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 13/48 (27%), Positives = 23/48 (47%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
           GFG+V++   E A +A++   G +V G K+ V+ +          S 
Sbjct: 50 MGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKPASGPSS 97

>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 Length = 114

 Score = 68.8 bits (169), Expect = 2e-14
 Identities = 21/85 (24%), Positives = 33/85 (38%), Gaps = 1/85 (1%)

Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDA 271
            +     L I N+P      E+++M  P G V +  I  +  +G S+G  F +       
Sbjct: 21  QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKC 79

Query: 272 ESAIQKFNGQKFGKRPIAVDWAVPK 296
           E+ I  FNG+     P       P 
Sbjct: 80  EAVIGHFNGKFIKTPPGVSAPTEPL 104

>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 Length = 114

 Score = 62.7 bits (153), Expect = 3e-12
 Identities = 24/102 (23%), Positives = 42/102 (41%), Gaps = 11/102 (10%)

Query: 417 QTEGEDELQNT-IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFK 475
           Q   + E   T ++I NLP  +D +E++     FG+V+S   +L   +   +G GF + +
Sbjct: 16  QMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVIS-TRILRDSSGTSRGVGFARME 74

Query: 476 TVEAATAAVSASKTTSGL-GIFLKGRQLTVLKA--LDKKLAH 514
           + E   A +          G F+K           L  K + 
Sbjct: 75  STEKCEAVIGH------FNGKFIKTPPGVSAPTEPLLCKFSG 110

>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 Length = 114

 Score = 43.4 bits (103), Expect = 2e-05
 Identities = 6/36 (16%), Positives = 10/36 (27%)

Query: 11  RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           RG G+ +    E     +   NG  +          
Sbjct: 66  RGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT 101

>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 Length = 205

 Score = 71.3 bits (174), Expect = 2e-14
 Identities = 33/234 (14%), Positives = 60/234 (25%), Gaps = 50/234 (21%)

Query: 426 NTIFICNL-PFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
             + +  L    ++ + V   F  +G V           K   G   ++     A   A+
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVK-----FMKSKPGAAMVEMADGYAVDRAI 59

Query: 485 SASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTP 544
           +           L    +       +K+     +  SK         Y         G  
Sbjct: 60  TH----------LNNNFMF-----GQKM----NVCVSKQPAIMPGQSY---------GLE 91

Query: 545 AAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSMTEKGLKKLCIDAVVS 604
                  D    R           ++   H S   L  +N P  +TE+   ++C      
Sbjct: 92  DGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNV-LHFFNAPLEVTEENFFEIC------ 144

Query: 605 RASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
               +  V +         K +            +E+     AL  L  LN+  
Sbjct: 145 ---DELGVKRPTSVKVFSGKSE------RSSSGLLEWDSKSDALETLGFLNHYQ 189

>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 Length = 205

 Score = 57.4 bits (138), Expect = 1e-09
 Identities = 8/78 (10%), Positives = 22/78 (28%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
             L   N P +       ++   +G+     +   +          +++  K DA   + 
Sbjct: 124 NVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLG 183

Query: 277 KFNGQKFGKRPIAVDWAV 294
             N  +         + +
Sbjct: 184 FLNHYQMKNPNGPYPYTL 201

>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 Length = 205

 Score = 55.9 bits (134), Expect = 6e-09
 Identities = 18/136 (13%), Positives = 37/136 (27%), Gaps = 3/136 (2%)

Query: 351 DEEVDIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKS 410
              VD A   LN        +  +           +    +  + S K    S+ N   +
Sbjct: 52  GYAVDRAITHLNNNFMFGQKMN-VCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFST 110

Query: 411 KPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTG 470
             ++ K         N +   N P ++  E   +     G        +         +G
Sbjct: 111 PEQAAKNRI--QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSG 168

Query: 471 FLKFKTVEAATAAVSA 486
            L++ +   A   +  
Sbjct: 169 LLEWDSKSDALETLGF 184

>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 Length = 205

 Score = 53.6 bits (128), Expect = 3e-08
 Identities = 15/86 (17%), Positives = 28/86 (32%), Gaps = 10/86 (11%)

Query: 209 GEGSKTQKWKLIIRNI-PFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G  S      L++  +   K   + + ++F   G V  V    +       G A V+   
Sbjct: 1   GADSPV----LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMAD 51

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWA 293
               + AI   N      + + V  +
Sbjct: 52  GYAVDRAITHLNNNFMFGQKMNVCVS 77

>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 Length = 261

 Score = 71.6 bits (176), Expect = 5e-14
 Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 7/92 (7%)

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
           GE + TQ+ +L + N+P      + K +F   G    V+I         +GF F++   +
Sbjct: 15  GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESR 68

Query: 269 RDAESAIQKFNGQKFGKRPIAVDWAVP-KNIY 299
             AE A  + +G     RP+ + +A     + 
Sbjct: 69  TLAEIAKAELDGTILKSRPLRIRFATHGAALT 100

>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 Length = 261

 Score = 63.2 bits (154), Expect = 3e-11
 Identities = 36/213 (16%), Positives = 65/213 (30%), Gaps = 43/213 (20%)

Query: 93  GKTVKPRKAATLGIDLADKEDCSQKQRVARTVIIGGLLNADMAEE-VHRLAGSIGTVCSV 151
           G T+  +            +   +       + +G L   D+ EE   RL    G    V
Sbjct: 3   GFTIDIKSFL---------KPGEKTYTQRCRLFVGNL-PTDITEEDFKRLFERYGEPSEV 52

Query: 152 TYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGTV---WARQLG 208
                +      G            +   +   A  + A L    +K   +   +A    
Sbjct: 53  FINRDR------GFG---------FIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGA 97

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
                     L ++N+        ++  FS  G V    +  + D G + G  FV+F  K
Sbjct: 98  ---------ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAK 147

Query: 269 RDAESAIQKFNGQKF----GKRPIAVDWAVPKN 297
             A  A+++     F      RP+ V+     +
Sbjct: 148 PPARKALERCGDGAFLLTTTPRPVIVEPMEQFD 180

>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 Length = 261

 Score = 58.2 bits (141), Expect = 2e-09
 Identities = 24/107 (22%), Positives = 40/107 (37%), Gaps = 7/107 (6%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           + + NL   + NE ++Q FS FG V     V+     R  G GF++F     A  A+   
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEK-AVVVVDDRGRATGKGFVEFAAKPPARKALERC 157

Query: 488 KTTSGLGIFLKGRQLTVLKA--LDKKLAHDKEIDKSKNETNDHRNLY 532
                 G FL       +    +++    D   +K   +T  +    
Sbjct: 158 GD----GAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKER 200

>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 Length = 261

 Score = 53.9 bits (130), Expect = 5e-08
 Identities = 27/100 (27%), Positives = 42/100 (42%), Gaps = 15/100 (15%)

Query: 410 SKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS-FVPVLHQVTKRPKG 468
                LK  E     +  +F+ NLP D+  E+ K+ F  +GE    F+        R +G
Sbjct: 7   DIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN-------RDRG 59

Query: 469 TGFLKFKTVEAATAAVSASKTTSGL-GIFLKGRQLTVLKA 507
            GF++ ++   A  A +       L G  LK R L +  A
Sbjct: 60  FGFIRLESRTLAEIAKAE------LDGTILKSRPLRIRFA 93

>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 Length = 261

 Score = 45.1 bits (107), Expect = 3e-05
 Identities = 13/42 (30%), Positives = 22/42 (52%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASL 52
          RGFG+++      A  A    +GT +  R + ++ A H A+L
Sbjct: 58 RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAAL 99

>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 Length = 196

 Score = 70.0 bits (172), Expect = 6e-14
 Identities = 21/122 (17%), Positives = 44/122 (36%), Gaps = 6/122 (4%)

Query: 390 DKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAF 449
           D  +N      D   +   ++  +   Q  G       IF+  +  D +   ++  F  +
Sbjct: 69  DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128

Query: 450 GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALD 509
           G++     +  + + + +G  F+ F   ++    V     T      + G    V KAL 
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT------VNGHNCEVRKALS 182

Query: 510 KK 511
           K+
Sbjct: 183 KQ 184

>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 Length = 196

 Score = 63.1 bits (154), Expect = 1e-11
 Identities = 28/110 (25%), Positives = 49/110 (44%), Gaps = 17/110 (15%)

Query: 402 VSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQ 461
           +SK  S K   +  K           +FI  L F+  +E ++  F  +G +   V +   
Sbjct: 1   MSKSESPKEPEQLRK-----------LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP 49

Query: 462 VTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
            TKR +G GF+ + TVE   AA++A          + GR +   +A+ ++
Sbjct: 50  NTKRSRGFGFVTYATVEEVDAAMNARPHK------VDGRVVEPKRAVSRE 93

>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 Length = 196

 Score = 56.5 bits (137), Expect = 3e-09
 Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           Q  KL I  + F+     ++  F   G + +  +  + +T  S+GF FV +    + ++A
Sbjct: 12  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71

Query: 275 IQKFNGQKFGKRPIAVDWAVPK 296
           +      K   R +    AV +
Sbjct: 72  MNA-RPHKVDGRVVEPKRAVSR 92

>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 Length = 196

 Score = 55.4 bits (134), Expect = 5e-09
 Identities = 25/136 (18%), Positives = 50/136 (36%), Gaps = 8/136 (5%)

Query: 177 VLYTTVKSACASVALLHQKEIKGGTVWAR------QLGGEGSKTQKWKLIIRNIPFKAKV 230
           V Y TV+   A++      ++ G  V  +           G+     K+ +  I    + 
Sbjct: 60  VTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEE 118

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
           + ++D F   G +  + I  +  +G  +GFAFV F      +  + +            V
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEV 177

Query: 291 DWAVPKNIYSSGGAAA 306
             A+ K   +S  ++ 
Sbjct: 178 RKALSKQEMASASSSQ 193

>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 Length = 196

 Score = 43.8 bits (104), Expect = 4e-05
 Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
           ++T +GS + RGF +V F   +  ++ V  K  T V G    V+ A+ +  +    S 
Sbjct: 136 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VNGHNCEVRKALSKQEMASASSS 192

>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 Length = 196

 Score = 42.3 bits (100), Expect = 2e-04
 Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 2   VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQ 61
           +    +   RGFG+V +A +E+ + A+  +    V GR +  K A+ R   ++  + +T 
Sbjct: 46  MRDPNTKRSRGFGFVTYATVEEVDAAMNAR-PHKVDGRVVEPKRAVSREDSQRPGAHLTV 104

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 66.8 bits (163), Expect = 6e-14
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 5/79 (6%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            + + N+P  A+V+++K     +G V     P        +  AF+ +     A+ A+  
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVSC 75

Query: 278 FNGQKFGKRPIAVDWAVPK 296
             G + G   + V  A  +
Sbjct: 76  LQGLRLGTDTLRVALARQQ 94

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 55.6 bits (134), Expect = 5e-10
 Identities = 25/99 (25%), Positives = 37/99 (37%), Gaps = 12/99 (12%)

Query: 406 NSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKR 465
           +S  S P S         L   +++ NLP D    ++K+     G V      L    + 
Sbjct: 2   SSGSSGPGSPPGEG--APLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQG 54

Query: 466 PKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV 504
           P+   FL +    AA  AVS  +     G+ L    L V
Sbjct: 55  PRRRAFLHYPDSAAAQQAVSCLQ-----GLRLGTDTLRV 88

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 42.5 bits (100), Expect = 3e-05
 Identities = 11/51 (21%), Positives = 18/51 (35%), Gaps = 6/51 (11%)

Query: 8  NEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
             R   ++ +     A +AV    G  +G   + V  A       Q+R K
Sbjct: 53 QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA------RQQRDK 97

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 67.1 bits (164), Expect = 7e-14
 Identities = 19/67 (28%), Positives = 33/67 (49%)

Query: 220 IIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN 279
           +I +         +  +FS  G V N+  P +  TG +KGF FV+     DA+  I+ F+
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 280 GQKFGKR 286
           G++   +
Sbjct: 76  GKRLDLK 82

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 49.7 bits (119), Expect = 7e-08
 Identities = 12/69 (17%), Positives = 27/69 (39%), Gaps = 6/69 (8%)

Query: 424 LQNTIFICNLP------FDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTV 477
               I +   P        +  + +   FS  G+VV+    + + T + KG  F++  ++
Sbjct: 5   SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSM 64

Query: 478 EAATAAVSA 486
             A   + +
Sbjct: 65  NDAKKIIKS 73

>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 Length = 103

 Score = 66.9 bits (164), Expect = 9e-14
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 8/89 (8%)

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
           G     +   L +RN+        ++  FS  G +  V           K +AF+ F  +
Sbjct: 4   GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDER 55

Query: 269 RDAESAIQKFNGQKFGKRPIAVDWAVPKN 297
             A  A+++ NG+      I + +A P +
Sbjct: 56  DGAVKAMEEMNGKDLEGENIEIVFAKPPD 84

>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 Length = 103

 Score = 51.1 bits (123), Expect = 3e-08
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 13/82 (15%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             +F+ NL   +  E +++ FS FG++           K+ K   F+ F   + A  A+ 
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIHFDERDGAVKAME 63

Query: 486 ASKTTSGLGIFLKGRQLTVLKA 507
                   G  L+G  + ++ A
Sbjct: 64  EMN-----GKDLEGENIEIVFA 80

>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 Length = 103

 Score = 44.2 bits (105), Expect = 8e-06
 Identities = 10/48 (20%), Positives = 20/48 (41%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
          + + ++ F   + A +A+E  NG  + G  I +  A       + R  
Sbjct: 45 KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKA 92

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 67.2 bits (164), Expect = 9e-14
 Identities = 25/107 (23%), Positives = 44/107 (41%), Gaps = 14/107 (13%)

Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWN----VYIPHNTDTGLSKGFAFVKFTC 267
           SK  +  + +R +PF A   E+   F     +      +      D G   G AFV F C
Sbjct: 19  SKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD-GRPTGDAFVLFAC 77

Query: 268 KRDAESAIQKFNGQKFGKRPIAV--------DWAVPKNIYSSGGAAA 306
           +  A++A++K +    GKR I +           + +   +SG ++ 
Sbjct: 78  EEYAQNALRK-HKDLLGKRYIELFRSTAAEVQQVLNRFSSASGPSSG 123

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 56.4 bits (136), Expect = 7e-10
 Identities = 24/105 (22%), Positives = 35/105 (33%), Gaps = 9/105 (8%)

Query: 406 NSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTK- 464
            SS     +        E Q  + +  LPF    EEV   F     +      +  VT  
Sbjct: 4   GSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP 63

Query: 465 --RPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
             RP G  F+ F   E A  A+   K        L  R + + ++
Sbjct: 64  DGRPTGDAFVLFACEEYAQNALRKHKD------LLGKRYIELFRS 102

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 39.1 bits (91), Expect = 7e-04
 Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 1/45 (2%)

Query: 2   VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
                     G  +V FA  E A  A+  K+   +G R I +  +
Sbjct: 59  FVTYPDGRPTGDAFVLFACEEYAQNALR-KHKDLLGKRYIELFRS 102

>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 Length = 109

 Score = 66.6 bits (163), Expect = 1e-13
 Identities = 18/83 (21%), Positives = 31/83 (37%), Gaps = 6/83 (7%)

Query: 223 NIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK 282
            I        ++  FSP G +  + +         KG++FV+F+    A  AI   NG  
Sbjct: 32  GIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTT 85

Query: 283 FGKRPIAVDWAVPKNIYSSGGAA 305
                +   W       +SG ++
Sbjct: 86  IEGHVVKCYWGKESPDMTSGPSS 108

>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 Length = 109

 Score = 51.9 bits (125), Expect = 2e-08
 Identities = 19/103 (18%), Positives = 41/103 (39%), Gaps = 13/103 (12%)

Query: 403 SKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS-FVPVLHQ 461
           S  + +  + +             T++   +   L ++ ++Q FS FG+++   V     
Sbjct: 3   SGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF---- 58

Query: 462 VTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV 504
                KG  F++F T E+A  A+ +       G  ++G  +  
Sbjct: 59  ---PEKGYSFVRFSTHESAAHAIVSVN-----GTTIEGHVVKC 93

>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 Length = 109

 Score = 46.9 bits (112), Expect = 8e-07
 Identities = 11/48 (22%), Positives = 21/48 (43%)

Query: 10  HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
            +G+ +V+F+  E A  A+   NGT++ G  +          +    S
Sbjct: 60  EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPS 107

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 66.1 bits (162), Expect = 1e-13
 Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 3/82 (3%)

Query: 217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIP-HNTDTGLSKGFAFVKFTCKRDAESAI 275
           +   + N+P+      IK+ F  +  +  V +P   ++    KGF + +F       SA+
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78

Query: 276 QKFNGQKFGKRPIAVDWAVPKN 297
              N +  G R I VD A    
Sbjct: 79  -SLNEESLGNRRIRVDVADQAQ 99

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 21/86 (24%), Positives = 42/86 (48%), Gaps = 8/86 (9%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSF-VPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           T F+ NLP+D+  E +K+ F     + +  +P      +R KG G+ +F+ +++  +A+S
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKK 511
            +         L  R++ V  A   +
Sbjct: 80  LN------EESLGNRRIRVDVADQAQ 99

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 47.2 bits (113), Expect = 6e-07
 Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 1/39 (2%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
          +GFGY +F  ++    A+ + N  S+G R+I V  A   
Sbjct: 61 KGFGYAEFEDLDSLLSALSL-NEESLGNRRIRVDVADQA 98

>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 Length = 167

 Score = 67.9 bits (167), Expect = 2e-13
 Identities = 18/91 (19%), Positives = 41/91 (45%), Gaps = 6/91 (6%)

Query: 420 GEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
            E +    IF+  +  D+  +E ++ FS +G ++    +L + T + +G GF+ + + +A
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 480 ATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
                          I  K R++ + +A  +
Sbjct: 142 VDRVCQNK------FIDFKDRKIEIKRAEPR 166

>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 Length = 167

 Score = 61.4 bits (150), Expect = 3e-11
 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 7/85 (8%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            +FI  L +D   + +++ F  +G V     +    T R +G GFL F+   +    V  
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64

Query: 487 SKTTSGLGIFLKGRQLTVLKALDKK 511
                     L G+ +   +A+ + 
Sbjct: 65  QHI-------LDGKVIDPKRAIPRD 82

>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 Length = 167

 Score = 60.2 bits (147), Expect = 7e-11
 Identities = 24/121 (19%), Positives = 47/121 (38%), Gaps = 3/121 (2%)

Query: 177 VLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDM 236
           + +    S    V   H   + G  +  ++      + +  K+ +  I    +  E ++ 
Sbjct: 50  LSFEKPSSVDEVVKTQH--ILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEF 107

Query: 237 FSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           FS  G + +  +  + DTG S+GF FV +      +   Q      F  R I +  A P+
Sbjct: 108 FSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIKRAEPR 166

Query: 297 N 297
           +
Sbjct: 167 H 167

>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 Length = 167

 Score = 56.4 bits (137), Expect = 2e-09
 Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           +  K+ I  + +    + +++ F   G V ++ I  +  TG S+GF F+ F      +  
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 275 IQKFNGQKFGKRPIAVDWAVPKN 297
           ++  +      + I    A+P++
Sbjct: 62  VKTQH--ILDGKVIDPKRAIPRD 82

>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 Length = 167

 Score = 44.1 bits (105), Expect = 3e-05
 Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           ++  K + + RGFG+V +   +  +R  + K       RKI +K A
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADAVDRVCQNK-FIDFKDRKIEIKRA 163

>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 Length = 167

 Score = 42.5 bits (101), Expect = 8e-05
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 10/75 (13%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK-- 58
           ++    +   RGFG++ F      +    +K    + G+ I  K A+ R   EQ ++   
Sbjct: 35  IMKDPATGRSRGFGFLSFEKPSSVDEV--VKTQHILDGKVIDPKRAIPRD--EQDKTGKI 90

Query: 59  ----VTQEVQAEDIE 69
               +  +V+ ++ E
Sbjct: 91  FVGGIGPDVRPKEFE 105

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 66.5 bits (162), Expect = 2e-13
 Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 221 IRNIPFKAKVNEIKDMFSP---VGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +R +P+   + ++++  S       V  V+  +  + G   G AFV+   + D + A++K
Sbjct: 22  LRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKK 80

Query: 278 FNGQKFGKRPIAV 290
            + +  G R I V
Sbjct: 81  -DRESMGHRYIEV 92

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 52.6 bits (126), Expect = 1e-08
 Identities = 17/100 (17%), Positives = 36/100 (36%), Gaps = 8/100 (8%)

Query: 410 SKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFG--EVVSFVPVLHQVTKRPK 467
           S   S      E      + +  LP+    E+V+   S     + V+ V  ++    R  
Sbjct: 2   SSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQS 61

Query: 468 GTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
           G  F++ ++ +    A+   +        +  R + V K+
Sbjct: 62  GEAFVELESEDDVKLALKKDRE------SMGHRYIEVFKS 95

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 39.1 bits (91), Expect = 5e-04
 Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 1/42 (2%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
                    G  +V+    +D   A++ K+  S+G R I V
Sbjct: 52 FIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV 92

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 65.4 bits (160), Expect = 3e-13
 Identities = 22/99 (22%), Positives = 40/99 (40%), Gaps = 3/99 (3%)

Query: 199 GGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSK 258
           G  +    + G  S T    L I N+     V E+K   S +    ++ +  +  TG ++
Sbjct: 1   GSHMLEDPVEGSESTTPF-NLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNR 58

Query: 259 GFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKN 297
            F +V F    D E A++   G K     I ++    ++
Sbjct: 59  KFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRD 96

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 62.3 bits (152), Expect = 3e-12
 Identities = 17/91 (18%), Positives = 35/91 (38%), Gaps = 7/91 (7%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
           E      +FI NL  +    E+K   S        + V+   T   +  G++ F++ E  
Sbjct: 13  ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDL 71

Query: 481 TAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
             A+  +      G+ + G ++ + K   + 
Sbjct: 72  EKALELT------GLKVFGNEIKLEKPKGRD 96

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
          V    +  +R FGYV F   ED  +A+E+  G  V G +I ++    R
Sbjct: 49 VVDVRTGTNRKFGYVDFESAEDLEKALEL-TGLKVFGNEIKLEKPKGR 95

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 64.6 bits (158), Expect = 4e-13
 Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 6/74 (8%)

Query: 232 EIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD 291
            ++  FSP G + ++ +         +  AFV +     A+ A+ + NG +     + V+
Sbjct: 29  LLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN 82

Query: 292 WAVPKNIYSSGGAA 305
            A  + +  SG ++
Sbjct: 83  IARKQPMLDSGPSS 96

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 13/80 (16%)

Query: 407 SSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRP 466
           SS S  +     +G     NT+++     D+    ++  FS FG ++            P
Sbjct: 2   SSGSSGERRAPRKG-----NTLYVYGE--DMTPTLLRGAFSPFGNIIDLS------MDPP 48

Query: 467 KGTGFLKFKTVEAATAAVSA 486
           +   F+ ++ +E+A  AV+ 
Sbjct: 49  RNCAFVTYEKMESADQAVAE 68

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 47.7 bits (114), Expect = 4e-07
 Identities = 14/45 (31%), Positives = 22/45 (48%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQ 54
           R   +V +  ME A++AV   NGT V   ++ V  A  +  L+ 
Sbjct: 48 PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDS 92

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 65.3 bits (159), Expect = 5e-13
 Identities = 22/117 (18%), Positives = 46/117 (39%), Gaps = 9/117 (7%)

Query: 406 NSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKR 465
           +    +   +  +         I I  LP D+   EV      FG+V + + +      +
Sbjct: 12  SGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------K 65

Query: 466 PKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSK 522
            K   F++  T EAA   V+   +       L+G+ + +  +  K+L  D   ++++
Sbjct: 66  GKNQAFIEMNTEEAANTMVNYYTSV---TPVLRGQPIYIQFSNHKELKTDSSPNQAR 119

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 52.2 bits (125), Expect = 2e-08
 Identities = 18/108 (16%), Positives = 39/108 (36%), Gaps = 12/108 (11%)

Query: 193 HQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNT 252
                +G  +   +  G  S+     + IR +P      E+  +  P G V N+ +    
Sbjct: 12  SGLVPRGSHMGDSRSAGVPSRV----IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG- 66

Query: 253 DTGLSKGFAFVKFTCKRDAESAIQKF--NGQKFGKRPIAVDWAVPKNI 298
                K  AF++   +  A + +  +         +PI + ++  K +
Sbjct: 67  -----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKEL 109

>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* ... Length = 97

 Score = 64.6 bits (158), Expect = 5e-13
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 7/82 (8%)

Query: 219 LIIRNIPFKAKVNEIK----DMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           + I N+  K K +E+K     +FS  G + ++ +     +   +G AFV F     A +A
Sbjct: 11  IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 67

Query: 275 IQKFNGQKFGKRPIAVDWAVPK 296
           ++   G  F  +P+ + +A   
Sbjct: 68  LRSMQGFPFYDKPMRIQYAKTD 89

>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* ... Length = 97

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 21/83 (25%), Positives = 42/83 (50%), Gaps = 12/83 (14%)

Query: 426 NTIFICNLPFDLDNEEVKQR----FSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAAT 481
           +TI+I NL   +  +E+K+     FS FG+++    +L   + + +G  F+ FK V +AT
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSAT 65

Query: 482 AAVSASKTTSGLGIFLKGRQLTV 504
            A+ + +     G     + + +
Sbjct: 66  NALRSMQ-----GFPFYDKPMRI 83

>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* ... Length = 97

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 10/63 (15%), Positives = 25/63 (39%), Gaps = 7/63 (11%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQ 61
          +    S + RG  +V F  +  A  A+    G     + + +++A       +  S +  
Sbjct: 42 ILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA-------KTDSDIIA 94

Query: 62 EVQ 64
          +++
Sbjct: 95 KMK 97

>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 Length = 108

 Score = 64.8 bits (158), Expect = 5e-13
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 7/86 (8%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           GG  S+  + ++++  +P      ++KD     G V    +          G   V+F  
Sbjct: 7   GGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVR 59

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWA 293
           K D   A++K +  KF        + 
Sbjct: 60  KEDMTYAVRKLDNTKFRSHEGETAYI 85

>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 Length = 108

 Score = 45.6 bits (108), Expect = 3e-06
 Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 14/84 (16%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           +N + +  LP     +++K      G+V  +  V         GTG ++F   E  T AV
Sbjct: 15  ENRVVVSGLPPSGSWQDLKDHMREAGDVC-YADV------YRDGTGVVEFVRKEDMTYAV 67

Query: 485 SASKTTSGL-GIFLKGRQLTVLKA 507
                   L     +  +      
Sbjct: 68  RK------LDNTKFRSHEGETAYI 85

>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 Length = 108

 Score = 42.5 bits (100), Expect = 3e-05
 Identities = 9/37 (24%), Positives = 13/37 (35%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
            G G V+F   ED   AV   + T     +    + 
Sbjct: 49 RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI 85

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 65.2 bits (159), Expect = 9e-13
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 5/84 (5%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTD-----TGLSKGFAFVKFTCKRDAE 272
           ++ ++N+    +  ++K +F       +       D      G  KG AF+    ++ A 
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 273 SAIQKFNGQKFGKRPIAVDWAVPK 296
            A+++ NG     +P+ V +A   
Sbjct: 107 KALKEANGYVLFGKPMVVQFARSA 130

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 54.8 bits (132), Expect = 3e-09
 Identities = 25/144 (17%), Positives = 54/144 (37%), Gaps = 10/144 (6%)

Query: 384 NKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVK 443
             + D   +   S +  +  +++  + +  S+ ++    E    I++ NL   +  +++K
Sbjct: 4   GSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLK 63

Query: 444 QRFSAFGEVVSFVP-----VLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK 498
             F  + +  S        +      R KG  F+     +AA  A+  +      G  L 
Sbjct: 64  YIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEAN-----GYVLF 118

Query: 499 GRQLTVLKALDKKLAHDKEIDKSK 522
           G+ + V  A   +   D +  K K
Sbjct: 119 GKPMVVQFARSARPKQDPKEGKRK 142

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 24/114 (21%), Positives = 47/114 (41%), Gaps = 12/114 (10%)

Query: 547 EGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIY--NLPKSMTEKGLKKLCIDAVVS 604
           E +S  ++ K ++  E+  T     ++        IY  NL K + EK LK +     V 
Sbjct: 13  ECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYI-FGRYVD 71

Query: 605 RASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP 658
            +S+ + ++  I+ ++  +          +G AF+     + A  AL+  N   
Sbjct: 72  FSSETQRIMFDIRLMKEGR---------MKGQAFIGLPNEKAAAKALKEANGYV 116

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 65.0 bits (158), Expect = 9e-13
 Identities = 21/102 (20%), Positives = 43/102 (42%), Gaps = 6/102 (5%)

Query: 193 HQKEIKGGTVWARQ-LGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSP---VGLVWNVYI 248
           H   + GG    R  +       + + + +R +P+   V ++++  S          V+ 
Sbjct: 20  HMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHF 79

Query: 249 PHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
            +  + G   G AFV+   + D + A++K + +  G R I V
Sbjct: 80  IYTRE-GRQSGEAFVELGSEDDVKMALKK-DRESMGHRYIEV 119

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 54.6 bits (131), Expect = 3e-09
 Identities = 15/110 (13%), Positives = 38/110 (34%), Gaps = 8/110 (7%)

Query: 400 SDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFG--EVVSFVP 457
           S ++ +   +   +       E      + +  LP+    E+V+   S     +  + V 
Sbjct: 19  SHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVH 78

Query: 458 VLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
            ++    R  G  F++  + +    A+   +        +  R + V K+
Sbjct: 79  FIYTREGRQSGEAFVELGSEDDVKMALKKDRE------SMGHRYIEVFKS 122

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 39.2 bits (91), Expect = 8e-04
 Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 1/42 (2%)

Query: 2   VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
                     G  +V+    +D   A++ K+  S+G R I V
Sbjct: 79  FIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV 119

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 63.3 bits (154), Expect = 1e-12
 Identities = 23/112 (20%), Positives = 44/112 (39%), Gaps = 9/112 (8%)

Query: 411 KPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTG 470
           +        G       I I  LP D+   EV      FG+V + + +      + K   
Sbjct: 2   RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQA 55

Query: 471 FLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSK 522
           F++  T EAA   V+   +       L+G+ + +  +  K+L  D   ++++
Sbjct: 56  FIEMNTEEAANTMVNYYTSV---TPVLRGQPIYIQFSNHKELKTDSSPNQAR 104

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 53.7 bits (129), Expect = 3e-09
 Identities = 18/104 (17%), Positives = 38/104 (36%), Gaps = 12/104 (11%)

Query: 197 IKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGL 256
           ++G         G  S+     + IR +P      E+  +  P G V N+ +        
Sbjct: 1   MRGSHHHHHHGSGVPSRV----IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG----- 51

Query: 257 SKGFAFVKFTCKRDAESAIQKF--NGQKFGKRPIAVDWAVPKNI 298
            K  AF++   +  A + +  +         +PI + ++  K +
Sbjct: 52  -KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKEL 94

>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} Length = 107

 Score = 62.9 bits (153), Expect = 2e-12
 Identities = 17/88 (19%), Positives = 42/88 (47%), Gaps = 10/88 (11%)

Query: 211 GSKTQK-----WKLIIRNIPFKAKVNEIKDMFSPVGLVW---NVYIPHNTDTGLSKGFAF 262
           GSK ++     + +  + +P+   + ++ + FS   +      ++   N D G  +G A 
Sbjct: 1   GSKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDAL 59

Query: 263 VKFTCKRDAESAIQKFNGQKFGKRPIAV 290
           ++   ++D + A++K +    G+R + V
Sbjct: 60  IEMESEQDVQKALEK-HRMYMGQRYVEV 86

>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} Length = 107

 Score = 49.9 bits (119), Expect = 1e-07
 Identities = 14/93 (15%), Positives = 33/93 (35%), Gaps = 10/93 (10%)

Query: 417 QTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFG--EVVSFVPVLHQVTKRPKGTGFLKF 474
           + E +D     I    LP+    E+V   FS        + +  L     + +G   ++ 
Sbjct: 5   EEEVDDVF--LIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEM 62

Query: 475 KTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
           ++ +    A+   +       ++  R + V + 
Sbjct: 63  ESEQDVQKALEKHRM------YMGQRYVEVYEI 89

>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} Length = 107

 Score = 38.7 bits (90), Expect = 7e-04
 Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 1/45 (2%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
                 + RG   ++    +D  +A+E K+   +G R + V   
Sbjct: 46 FLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYEI 89

>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 Length = 115

 Score = 62.9 bits (153), Expect = 3e-12
 Identities = 18/92 (19%), Positives = 33/92 (35%), Gaps = 7/92 (7%)

Query: 205 RQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVK 264
           R   G  S+  + ++++  +P      ++KD     G V    +          G   V+
Sbjct: 5   RGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVE 57

Query: 265 FTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           F  K D   A++K +  KF        +   K
Sbjct: 58  FVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 89

>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 Length = 115

 Score = 46.0 bits (109), Expect = 3e-06
 Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 14/84 (16%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           +N + +  LP     +++K      G+V  +  V         GTG ++F   E  T AV
Sbjct: 16  ENRVVVSGLPPSGSWQDLKDHMREAGDVC-YADV------YRDGTGVVEFVRKEDMTYAV 68

Query: 485 SASKTTSGL-GIFLKGRQLTVLKA 507
                   L     +  +      
Sbjct: 69  RK------LDNTKFRSHEGETAYI 86

>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 Length = 115

 Score = 42.5 bits (100), Expect = 4e-05
 Identities = 10/48 (20%), Positives = 16/48 (33%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
            G G V+F   ED   AV   + T     +    +   +    +  S
Sbjct: 50 RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPS 97

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 61.6 bits (150), Expect = 3e-12
 Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 8/74 (10%)

Query: 219 LIIRNIP------FKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAE 272
           +++ N+P       +   N I  +FS  G + N + P   + G +KG+ F+++     A 
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAV 61

Query: 273 SAIQKFNGQKFGKR 286
            A++  +G K  K+
Sbjct: 62  DAVKNADGYKLDKQ 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 8/67 (11%)

Query: 426 NTIFICNLP------FDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
           + I + N+P       +     + + FS FG++ +      +   + KG  FL++ +   
Sbjct: 2   SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDF--YPEEDGKTKGYIFLEYASPAH 59

Query: 480 ATAAVSA 486
           A  AV  
Sbjct: 60  AVDAVKN 66

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 62.2 bits (152), Expect = 3e-12
 Identities = 21/92 (22%), Positives = 41/92 (44%), Gaps = 6/92 (6%)

Query: 420 GEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
                 N IF+  +P +    E+++ F  FG V   V +     +RP+G GF+ F+  ++
Sbjct: 5   SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQS 64

Query: 480 ATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
              AV+           + G+++ V +A  + 
Sbjct: 65  VDQAVNMHFHD------IMGKKVEVKRAEPRD 90

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 55.3 bits (134), Expect = 8e-10
 Identities = 20/95 (21%), Positives = 45/95 (47%), Gaps = 1/95 (1%)

Query: 211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRD 270
            S ++  K+ +  IP      E+++ F   G+V  V + ++ +    +GF F+ F  ++ 
Sbjct: 5   SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQS 64

Query: 271 AESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAA 305
            + A+   +      + + V  A P++  SSG ++
Sbjct: 65  VDQAVNM-HFHDIMGKKVEVKRAEPRDSKSSGPSS 98

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 41.0 bits (97), Expect = 8e-05
 Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          M+        RGFG++ F   +  ++AV M +   + G+K+ VK A  R S     S
Sbjct: 42 MIYDAEKQRPRGFGFITFEDEQSVDQAVNM-HFHDIMGKKVEVKRAEPRDSKSSGPS 97

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.1 bits (151), Expect = 4e-12
 Identities = 22/104 (21%), Positives = 45/104 (43%), Gaps = 7/104 (6%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
            D    +++I   P D   +++K+     G+V++ + +   + K  KG+ F+ F ++E+A
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESA 65

Query: 481 TAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNE 524
              V             K   L +L   D     ++E  ++K E
Sbjct: 66  KKFVETPGQK------YKETDLLILFKDDYFAKKNEERKQNKVE 103

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 50.9 bits (122), Expect = 3e-08
 Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            + I+  P  A +++IK+     G V N+ +         KG  FV F     A+  ++ 
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVET 71

Query: 278 FNGQKFGKRPIAVDWA 293
             GQK+ +  + + + 
Sbjct: 72  -PGQKYKETDLLILFK 86

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 62.1 bits (151), Expect = 4e-12
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 8/75 (10%)

Query: 218 KLIIRNIPFKAK------VNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDA 271
            +++ N+P           N I  +FS  G + N + P   + G +KG+ F+++     A
Sbjct: 17  VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHA 74

Query: 272 ESAIQKFNGQKFGKR 286
             A++  +G K  K+
Sbjct: 75  VDAVKNADGYKLDKQ 89

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 48.6 bits (116), Expect = 3e-07
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 8/77 (10%)

Query: 416 KQTEGEDELQNTIFICNLP------FDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGT 469
            + +  D + + I + N+P       +     + + FS FG++ +      +   + KG 
Sbjct: 6   DRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDF--YPEEDGKTKGY 63

Query: 470 GFLKFKTVEAATAAVSA 486
            FL++ +   A  AV  
Sbjct: 64  IFLEYASPAHAVDAVKN 80

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 61.9 bits (151), Expect = 5e-12
 Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 8/86 (9%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           NT+F+  +   +D  E++  F+ +G V   V ++   T   KG GF+ F         V 
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKE-VKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKK 511
           +            G++L +  A+ K+
Sbjct: 69  SQIN-------FHGKKLKLGPAIRKQ 87

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 5/80 (6%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTD-TGLSKGFAFVKFTCKRDAESAIQ 276
            + +  I  +    EI+  F+  G V  V I   TD TG+SKG+ FV F    D +  ++
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKII--TDRTGVSKGYGFVSFYNDVDVQKIVE 68

Query: 277 KFNGQKFGKRPIAVDWAVPK 296
             +   F  + + +  A+ K
Sbjct: 69  --SQINFHGKKLKLGPAIRK 86

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 11/52 (21%), Positives = 25/52 (48%), Gaps = 2/52 (3%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
          +   +G+G+V F    D  + VE  +  +  G+K+ +  A+ + +L     +
Sbjct: 46 TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIRKQNLSTYHVQ 95

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 60.9 bits (148), Expect = 6e-12
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 11/82 (13%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFV-----PVLHQVTKRPKGTGFLKFKTVEAATA 482
           +++ N+PF +  E +   F+A   +         PVL     + K   FL+F++V+  T 
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 483 AVSASKTTSGLGIFLKGRQLTV 504
           A++        GI  +G+ L +
Sbjct: 69  AMAFD------GIIFQGQSLKI 84

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 57.4 bits (139), Expect = 1e-10
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIP-----HNTDTGLSKGFAFVKFTCKRDAE 272
           +L + NIPF      + D F+    +  +                K FAF++F    +  
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 273 SAIQKFNGQKFGKRPIAV 290
            A+  F+G  F  + + +
Sbjct: 68  QAMA-FDGIIFQGQSLKI 84

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 40.9 bits (96), Expect = 6e-05
 Identities = 7/43 (16%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 2  VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVK 44
          V     N+ + F +++F  +++  +A+   +G    G+ + ++
Sbjct: 44 VLAVQINQDKNFAFLEFRSVDETTQAMAF-DGIIFQGQSLKIR 85

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 62.2 bits (151), Expect = 7e-12
 Identities = 13/83 (15%), Positives = 37/83 (44%), Gaps = 7/83 (8%)

Query: 218 KLIIRNIPFKAKVNEIK----DMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAES 273
            ++I NI  +    +++     + S  G + ++ +     +  + G A++ F  +  A++
Sbjct: 31  VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQA 87

Query: 274 AIQKFNGQKFGKRPIAVDWAVPK 296
            ++ F G  F   P+ + ++   
Sbjct: 88  FVEAFQGYPFQGNPLVITFSETP 110

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 54.1 bits (130), Expect = 5e-09
 Identities = 17/108 (15%), Positives = 45/108 (41%), Gaps = 18/108 (16%)

Query: 426 NTIFICNLPFDLDNEEVKQ----RFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAAT 481
             + I N+  ++  E+++       S+ G+++    ++  ++    G  ++ F T E+A 
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLSDDNSGKAYIVFATQESAQ 86

Query: 482 AAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHR 529
           A V A +     G   +G  L +        +   +   +++ + +H 
Sbjct: 87  AFVEAFQ-----GYPFQGNPLVI------TFSETPQSQVAEDGSLEHH 123

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 61.4 bits (149), Expect = 7e-12
 Identities = 15/86 (17%), Positives = 34/86 (39%), Gaps = 3/86 (3%)

Query: 205 RQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVK 264
           R         +++++ ++N+P      ++KD+     L    +   NT      G   ++
Sbjct: 17  RGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE-TTFSSVNTRD--FDGTGALE 73

Query: 265 FTCKRDAESAIQKFNGQKFGKRPIAV 290
           F  +     A+++ N  +F    I V
Sbjct: 74  FPSEEILVEALERLNNIEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 50.2 bits (120), Expect = 6e-08
 Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 10/81 (12%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           +  I + NLP     +++K          +F  V    T+   GTG L+F + E    A+
Sbjct: 28  RYRITMKNLPEGCSWQDLKDLARENSLETTFSSV---NTRDFDGTGALEFPSEEILVEAL 84

Query: 485 SASKTTSGL-GIFLKGRQLTV 504
                   L  I  +G  +TV
Sbjct: 85  ER------LNNIEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 46.4 bits (110), Expect = 2e-06
 Identities = 10/43 (23%), Positives = 17/43 (39%)

Query: 2   VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVK 44
            +   + +  G G ++F   E    A+E  N     G  I V+
Sbjct: 58  FSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE 100

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 59.8 bits (146), Expect = 1e-11
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +FI  L +    E +++ F  FGEV   + +   +TKR +G GF+ F         ++ S
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 488 KTTSGLGIFLKGRQLTVLKAL 508
           +        L  + +    A 
Sbjct: 63  RHE------LDSKTIDPKVAF 77

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 38.6 bits (91), Expect = 3e-04
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ I  + ++     +++ F   G V    +  +  T  S+GF FV F  +   +  + +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 278 FNGQKFGKRPIAVDWA 293
            +  +   + I    A
Sbjct: 62  -SRHELDSKTIDPKVA 76

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 38.2 bits (90), Expect = 4e-04
 Identities = 9/42 (21%), Positives = 16/42 (38%), Gaps = 1/42 (2%)

Query: 5  KGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
            +   RGFG+V F      ++ +       +  + I  K A
Sbjct: 36 PLTKRSRGFGFVTFMDQAGVDKVLAQSRHE-LDSKTIDPKVA 76

>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 Length = 110

 Score = 60.1 bits (146), Expect = 3e-11
 Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 9/87 (10%)

Query: 218 KLIIRNIPF-KAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           ++ I N+     K ++++ +FS  G V    +         KG+AFV+++ +R A +A+ 
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVL 80

Query: 277 KFNGQKFGKRPIAVDWAVPKNIYSSGG 303
             NG+    + + ++ A       SG 
Sbjct: 81  GENGRVLAGQTLDINMAGEPKPDRSGP 107

>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 Length = 110

 Score = 48.1 bits (115), Expect = 4e-07
 Identities = 12/48 (25%), Positives = 22/48 (45%)

Query: 10  HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           H+G+ +VQ++    A  AV  +NG  + G+ + +  A          S
Sbjct: 61  HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPS 108

>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 Length = 110

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 25/106 (23%), Positives = 39/106 (36%), Gaps = 14/106 (13%)

Query: 400 SDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDL-DNEEVKQRFSAFGEVVSFVPV 458
           S  S   S K +  ++        + + +FI NL   L    +V+  FS +G V      
Sbjct: 2   SSGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAG---- 57

Query: 459 LHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV 504
                   KG  F+++     A AAV         G  L G+ L +
Sbjct: 58  ----CSVHKGYAFVQYSNERHARAAVLGEN-----GRVLAGQTLDI 94

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 7/77 (9%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L +  +       ++++ F   G +  + +         +  AF++F  ++ AE A +K
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEK 67

Query: 278 -FNGQKFGKRPIAVDWA 293
            FN      R + V W 
Sbjct: 68  SFNKLIVNGRRLNVKWG 84

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 21/85 (24%), Positives = 41/85 (48%), Gaps = 10/85 (11%)

Query: 420 GEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
           GED+   T+++  L   +   +++  F  FGE+ + + V+ +     +   F++F T +A
Sbjct: 7   GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRT-ITVVQR-----QQCAFIQFATRQA 60

Query: 480 ATAAVSASKTTSGLGIFLKGRQLTV 504
           A  A   S       + + GR+L V
Sbjct: 61  AEVAAEKSFN----KLIVNGRRLNV 81

>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 Length = 104

 Score = 59.4 bits (144), Expect = 3e-11
 Identities = 11/96 (11%), Positives = 34/96 (35%), Gaps = 9/96 (9%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + +  L   +   ++ +    FG +         +    K    ++F+ +++A   V+
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYV------MMMPFKRQALVEFENIDSAKECVT 69

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKS 521
            +       +++ G+Q     +  K++        S
Sbjct: 70  FAADV---PVYIAGQQAFFNYSTSKRITRPGNSGPS 102

>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 Length = 104

 Score = 51.7 bits (124), Expect = 2e-08
 Identities = 11/87 (12%), Positives = 26/87 (29%), Gaps = 8/87 (9%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           +R +       ++ +     G +  V +         K  A V+F     A+  +     
Sbjct: 20  VRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAAD 73

Query: 281 QKF--GKRPIAVDWAVPKNIYSSGGAA 305
                  +    +++  K I   G + 
Sbjct: 74  VPVYIAGQQAFFNYSTSKRITRPGNSG 100

>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 Length = 97

 Score = 58.8 bits (143), Expect = 4e-11
 Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 8/78 (10%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           +L +  +     +  +   F   G +  +             FA++++     A++A  K
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72

Query: 278 FNGQKFG--KRPIAVDWA 293
             G   G   R + VD+A
Sbjct: 73  MRGFPLGGPDRRLRVDFA 90

>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 Length = 97

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 8/61 (13%), Positives = 26/61 (42%), Gaps = 6/61 (9%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             +++  L  +     + + F  FG + +          +     ++++++++AA AA +
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTI------DHVKGDSFAYIQYESLDAAQAACA 71

Query: 486 A 486
            
Sbjct: 72  K 72

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 57.9 bits (141), Expect = 5e-11
 Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           IF+  L  +   E+VK  F  FG+V   + +  + T R +G GF+ F++ +         
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 488 KTTSGLGIFLKGRQLTVLKA 507
                    +  + +   KA
Sbjct: 62  FHE------INNKMVECKKA 75

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 39.4 bits (93), Expect = 2e-04
 Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 5  KGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          K +N HRGFG+V F   +   +  E+     +  + +  K A
Sbjct: 35 KTTNRHRGFGFVTFESEDIVEKVCEIHFHE-INNKMVECKKA 75

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 37.8 bits (89), Expect = 7e-04
 Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 1/76 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ +  +     V ++K  F   G V +  +  +  T   +GF FV F  +   E   + 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 278 FNGQKFGKRPIAVDWA 293
            +  +   + +    A
Sbjct: 61  -HFHEINNKMVECKKA 75

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 59.2 bits (144), Expect = 5e-11
 Identities = 22/101 (21%), Positives = 38/101 (37%), Gaps = 6/101 (5%)

Query: 410 SKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGT 469
           S   S      +D     IF+  LP+   +  +++ F  FG++   V +  + T + +G 
Sbjct: 2   SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGY 61

Query: 470 GFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
           GF+      AA  A             + GR+  V  A   
Sbjct: 62  GFVTMADRAAAERACKDPNPI------IDGRKANVNLAYLG 96

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 45.0 bits (107), Expect = 6e-06
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 1/97 (1%)

Query: 200 GTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKG 259
           G+  +  + G    T   K+ +  +P+      ++  F   G +    +  +  TG S+G
Sbjct: 1   GSSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 60

Query: 260 FAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
           + FV    +  AE A +  N      R   V+ A   
Sbjct: 61  YGFVTMADRAAAERACKDPN-PIIDGRKANVNLAYLG 96

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 41.5 bits (98), Expect = 9e-05
 Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 1/40 (2%)

Query: 11 RGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRA 50
          RG+G+V  A    A RA +  N   + GRK  V  A   A
Sbjct: 59 RGYGFVTMADRAAAERACKDPNPI-IDGRKANVNLAYLGA 97

>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 Length = 103

 Score = 58.8 bits (143), Expect = 6e-11
 Identities = 23/106 (21%), Positives = 39/106 (36%), Gaps = 13/106 (12%)

Query: 406 NSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKR 465
           +S  S  K         +  + + +  LP+    +++K+ FS FGEV+         T  
Sbjct: 2   SSGSSGVKR------AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGH 55

Query: 466 PKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
            KG GF++F   E     +S           + GR         K+
Sbjct: 56  SKGFGFVRFTEYETQVKVMSQRHM-------IDGRWCDCKLPNSKQ 94

>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 Length = 103

 Score = 48.0 bits (115), Expect = 4e-07
 Identities = 25/98 (25%), Positives = 42/98 (42%), Gaps = 2/98 (2%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G + +  +   LI+  +P+K    ++K+ FS  G V  V +  +  TG SKGF FV+FT 
Sbjct: 7   GVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE 66

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAA 305
                  + + +      R         K    SG ++
Sbjct: 67  YETQVKVMSQRH--MIDGRWCDCKLPNSKQSQDSGPSS 102

>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 Length = 103

 Score = 41.1 bits (97), Expect = 9e-05
 Identities = 11/56 (19%), Positives = 22/56 (39%), Gaps = 2/56 (3%)

Query: 2   VTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
                +   +GFG+V+F   E   + +  ++   + GR    K    + S +   S
Sbjct: 48  KKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQDSGPS 101

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 58.8 bits (143), Expect = 7e-11
 Identities = 22/108 (20%), Positives = 41/108 (37%), Gaps = 10/108 (9%)

Query: 404 KLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVT 463
             +SS   P+              +FI  L +    E +++ F  FGEV   + +   +T
Sbjct: 8   HHHSSGLVPRG----SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLT 63

Query: 464 KRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           KR +G GF+ F         ++ S+        L  + +    A  ++
Sbjct: 64  KRSRGFGFVTFMDQAGVDKVLAQSRHE------LDSKTIDPKVAFPRR 105

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 46.9 bits (112), Expect = 1e-06
 Identities = 16/88 (18%), Positives = 35/88 (39%), Gaps = 1/88 (1%)

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
           G    +   K+ I  + ++     +++ F   G V    +  +  T  S+GF FV F  +
Sbjct: 18  GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77

Query: 269 RDAESAIQKFNGQKFGKRPIAVDWAVPK 296
              +  + + +  +   + I    A P+
Sbjct: 78  AGVDKVLAQ-SRHELDSKTIDPKVAFPR 104

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 38.4 bits (90), Expect = 9e-04
 Identities = 10/45 (22%), Positives = 17/45 (37%), Gaps = 1/45 (2%)

Query: 5   KGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
             +   RGFG+V F      ++ +       +  + I  K A  R
Sbjct: 61  PLTKRSRGFGFVTFMDQAGVDKVLAQSRHE-LDSKTIDPKVAFPR 104

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 58.7 bits (142), Expect = 7e-11
 Identities = 21/94 (22%), Positives = 34/94 (36%), Gaps = 6/94 (6%)

Query: 215 QKWKLIIRNIPFKAKVNEI---KDMFSPVGLVWNVYIPHNTDTGLSK---GFAFVKFTCK 268
           QK  + +  +  +    E+    + F   G +  V I ++T    S+     A+V +   
Sbjct: 14  QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73

Query: 269 RDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSG 302
            DA  AIQ  N      R +       K    SG
Sbjct: 74  EDALRAIQCVNNVVVDGRTLKASLGTTKYCSYSG 107

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 45.6 bits (108), Expect = 3e-06
 Identities = 13/42 (30%), Positives = 17/42 (40%)

Query: 5  KGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           GS       YV +   EDA RA++  N   V GR +     
Sbjct: 57 AGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLG 98

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 11/85 (12%)

Query: 426 NTIFICNLPFDLDNEEV---KQRFSAFGEVVSFV---PVLHQVTKRPKGTGFLKFKTVEA 479
           N +F+  L   L + EV    + F  FG++   V      +  ++ P  + ++ +   E 
Sbjct: 16  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 480 ATAAVSASKTTSGLGIFLKGRQLTV 504
           A  A+          + + GR L  
Sbjct: 76  ALRAIQCVN-----NVVVDGRTLKA 95

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 58.2 bits (141), Expect = 8e-11
 Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 9/79 (11%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + I  L   +   ++ +    FG +   V +        K    ++F+ V  A  AV+
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVN 75

Query: 486 ASKTTSGLGIFLKGRQLTV 504
            +       I++ G    V
Sbjct: 76  YAADN---QIYIAGHPAFV 91

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 50.1 bits (120), Expect = 6e-08
 Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 8/80 (10%)

Query: 221 IRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG 280
           IR +       ++ +     G +  V +         K  A V+F     A +A+     
Sbjct: 26  IRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAAD 79

Query: 281 Q--KFGKRPIAVDWAVPKNI 298
                   P  V+++  + I
Sbjct: 80  NQIYIAGHPAFVNYSTSQKI 99

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 58.4 bits (142), Expect = 9e-11
 Identities = 23/114 (20%), Positives = 49/114 (42%), Gaps = 8/114 (7%)

Query: 397 AKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFV 456
                     + ++ P   K+ E E      +FI  L F+   E ++  +  +G++   V
Sbjct: 1   GSSGSSGMEKTLETVPLERKKREKEQF--RKLFIGGLSFETTEESLRNYYEQWGKLTDCV 58

Query: 457 PVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
            +    +KR +G GF+ F ++    AA++A   +      + GR +   +A+ +
Sbjct: 59  VMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHS------IDGRVVEPKRAVAR 106

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 46.9 bits (112), Expect = 1e-06
 Identities = 19/93 (20%), Positives = 40/93 (43%), Gaps = 1/93 (1%)

Query: 213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAE 272
           K Q  KL I  + F+     +++ +   G + +  +  +  +  S+GF FV F+   + +
Sbjct: 24  KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD 83

Query: 273 SAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAA 305
           +A+          R +    AV +    SG ++
Sbjct: 84  AAMAA-RPHSIDGRVVEPKRAVAREESGSGPSS 115

>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 Length = 87

 Score = 57.2 bits (139), Expect = 1e-10
 Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 6/87 (6%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
            +E    +F+  L +D   +++K  F+ FGEVV     +   T R +G GF+ FK   + 
Sbjct: 7   NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASV 66

Query: 481 TAAVSASKTTSGLGIFLKGRQLTVLKA 507
              +   +        L GR +   KA
Sbjct: 67  EKVLDQKEHR------LDGRVIDPKKA 87

>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 Length = 87

 Score = 41.0 bits (97), Expect = 7e-05
 Identities = 15/68 (22%), Positives = 30/68 (44%)

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
              ++    K+ +  + +     ++KD F+  G V +  I  + +TG S+GF F+ F   
Sbjct: 4   ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA 63

Query: 269 RDAESAIQ 276
              E  + 
Sbjct: 64  ASVEKVLD 71

>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 Length = 87

 Score = 38.3 bits (90), Expect = 5e-04
 Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 1/42 (2%)

Query: 5  KGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
            +   RGFG++ F       + ++ K    + GR I  K A
Sbjct: 47 PNTGRSRGFGFILFKDAASVEKVLDQKEHR-LDGRVIDPKKA 87

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 56.8 bits (138), Expect = 2e-10
 Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 9/80 (11%)

Query: 218 KLIIRNIPFK-AKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           +L I N+P K     ++  +FSP G +  + I           F F++F   +    AI+
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE 63

Query: 277 KFNGQKFGKRPIAVDWAVPK 296
             + +    + + ++ +   
Sbjct: 64  CESQEMNFGKKLILEVSSSN 83

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 46.8 bits (112), Expect = 7e-07
 Identities = 8/37 (21%), Positives = 19/37 (51%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
             FG++QF   +    A+E ++     G+K+ ++ +
Sbjct: 44 KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVS 80

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 15/87 (17%), Positives = 36/87 (41%), Gaps = 14/87 (16%)

Query: 426 NTIFICNLPF-DLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           + +FI NLP  ++  E++ + FS +G ++  + +           GF++F   ++   A+
Sbjct: 11  SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQ-INIK-------NAFGFIQFDNPQSVRDAI 62

Query: 485 SASKTTSGLGIFLKGRQLTVLKALDKK 511
                         G++L +  +    
Sbjct: 63  ECES-----QEMNFGKKLILEVSSSNA 84

>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 Length = 97

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 9/81 (11%)

Query: 218 KLIIRNIPF-KAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           +L I N+P       ++  +FSP G +  + I           F F++F   +    AI+
Sbjct: 24  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE 75

Query: 277 KFNGQKFGKRPIAVDWAVPKN 297
             + +    + + ++ +    
Sbjct: 76  XESQEMNFGKKLILEVSSSNA 96

>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 Length = 97

 Score = 46.9 bits (112), Expect = 6e-07
 Identities = 9/41 (21%), Positives = 20/41 (48%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRA 50
             FG++QF   +    A+E ++     G+K+ ++ +   A
Sbjct: 56 KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA 96

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 56.4 bits (136), Expect = 4e-10
 Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 9/79 (11%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + I  LP ++   EV      FG+V + + +      + K   FL+  T EAA   V+
Sbjct: 16  RVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELATEEAAITMVN 69

Query: 486 ASKTTSGLGIFLKGRQLTV 504
                      L+ + + +
Sbjct: 70  YYSAV---TPHLRNQPIYI 85

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 49.8 bits (119), Expect = 7e-08
 Identities = 18/86 (20%), Positives = 37/86 (43%), Gaps = 8/86 (9%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L IR +P +    E+  +  P G V N+ +         K  AF++   +  A + +  +
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILMLK------GKNQAFLELATEEAAITMVNYY 71

Query: 279 NGQK--FGKRPIAVDWAVPKNIYSSG 302
           +        +PI + ++  K + +SG
Sbjct: 72  SAVTPHLRNQPIYIQYSNHKELKTSG 97

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 56.1 bits (136), Expect = 5e-10
 Identities = 21/90 (23%), Positives = 38/90 (42%), Gaps = 6/90 (6%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
             +    +F+  L +    E ++  FS +GEVV  V +  + T + +G GF+KFK     
Sbjct: 12  GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCV 71

Query: 481 TAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
              +++   T      L GR +       +
Sbjct: 72  GTVLASRPHT------LDGRNIDPKPCTPR 95

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 1/97 (1%)

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
                 +  KL +  + +      ++  FS  G V +  I  +  T  S+GF FVKF   
Sbjct: 9   NNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68

Query: 269 RDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAA 305
               + +          R I      P+ +  SG ++
Sbjct: 69  NCVGTVLAS-RPHTLDGRNIDPKPCTPRGMQPSGPSS 104

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 1/47 (2%)

Query: 5  KGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRAS 51
          K +N+ RGFG+V+F         +  +  T + GR I  K    R  
Sbjct: 52 KTTNQSRGFGFVKFKDPNCVGTVLASRPHT-LDGRNIDPKPCTPRGM 97

>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 Length = 75

 Score = 54.8 bits (133), Expect = 7e-10
 Identities = 18/80 (22%), Positives = 31/80 (38%), Gaps = 6/80 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           IF+  L  D   E++++ F  FGEV S    +   T + +G  F+ FK  E     +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 488 KTTSGLGIFLKGRQLTVLKA 507
                    +   +  +  A
Sbjct: 62  YHN------VGLSKCEIKVA 75

>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 Length = 75

 Score = 40.9 bits (97), Expect = 4e-05
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ +  +       +I++ F   G V ++ +P +  T   +GF F+ F  +   +  ++K
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 278 FNGQKFGKRPIAVDWA 293
                 G     +  A
Sbjct: 61  -KYHNVGLSKCEIKVA 75

>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 Length = 75

 Score = 40.6 bits (96), Expect = 8e-05
 Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 1/46 (2%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          +     +N+ RGF ++ F   E   + +E K    VG  K  +K A
Sbjct: 31 LPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHN-VGLSKCEIKVA 75

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 55.7 bits (135), Expect = 7e-10
 Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 254 TGLSKGFAFVKFTCKRDAESAIQKFNGQKF-GKRPIAVDWAVPKN 297
           TG+SKG+ FVKFT + + + A+ +  G    G +P+ +  A+PK 
Sbjct: 47  TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKA 91

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 44.2 bits (105), Expect = 7e-06
 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 4/85 (4%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           ++F+ +L  D+D+  + + F           V+   T   KG GF+KF        A+  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRAL-- 68

Query: 487 SKTTSGLGIFLKGRQLTVLKALDKK 511
                G  + L  + + +  A+ K 
Sbjct: 69  -TECQG-AVGLGSKPVRLSVAIPKA 91

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 11/42 (26%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 11 RGFGYVQFAVMEDANRAV-EMKNGTSVGGRKIGVKHAMHRAS 51
          +G+G+V+F    +  RA+ E +    +G + + +  A+ +AS
Sbjct: 51 KGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKAS 92

>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 Length = 96

 Score = 53.8 bits (129), Expect = 3e-09
 Identities = 25/99 (25%), Positives = 43/99 (43%), Gaps = 7/99 (7%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIK----DMFSPVGLVWNVYIPHNTDTGLSKGFAFV 263
           G  GS      + + NI ++    E++    + F+  G V +V +  +TD    +  A V
Sbjct: 1   GSSGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTD---YQLKAVV 57

Query: 264 KFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSG 302
           +    +DA  A+   +  K G + I V  A   +  SSG
Sbjct: 58  QMENLQDAIGAVNSLHRYKIGSKKILVSLATGASGPSSG 96

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 58.7 bits (141), Expect = 5e-09
 Identities = 100/665 (15%), Positives = 176/665 (26%), Gaps = 229/665 (34%)

Query: 45  HAMHRASLE----QRRSKVTQEVQAEDIEKTMDNKD------GVISGAE-KHSSKLLESG 93
           H  H    E    Q + K    V  +      D KD       ++S  E  H   ++ S 
Sbjct: 2   HHHHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDH---IIMSK 58

Query: 94  KTVKPRKAATLGIDLADKEDCSQKQRVARTVIIGGLLNAD---MAEEVH----------- 139
             V       L   L  K    Q++ V + V    +L  +   +   +            
Sbjct: 59  DAVS--GTLRLFWTLLSK----QEEMVQKFV--EEVLRINYKFLMSPIKTEQRQPSMMTR 110

Query: 140 -------RLAGSIGTVC--SVTYPLPKEELEQ-------------HGLAQEGC-KMDASA 176
                  RL          +V+   P  +L Q              G+   G  K     
Sbjct: 111 MYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVL--GSGK----T 164

Query: 177 VLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKT----QKWKLIIR---------- 222
            +       C S  +  Q ++     W   L    S         KL+ +          
Sbjct: 165 WV---ALDVCLSYKV--QCKMDFKIFWLN-LKNCNSPETVLEMLQKLLYQIDPNWTSRSD 218

Query: 223 ---NIPFKAKVNEIKDMFS--------PVGL-----VWNVYIPHNTDTGLSKGFAFVKFT 266
              NI  +  ++ I+               L     V N              F     +
Sbjct: 219 HSSNIKLR--IHSIQAELRRLLKSKPYENCLLVLLNVQNAKA--------WNAF---NLS 265

Query: 267 CK-----RD----------------------------AESAIQKFNGQKFGKRPIAVDWA 293
           CK     R                              +S + K+   +    P  V   
Sbjct: 266 CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTT 325

Query: 294 VPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDS----NSSEK----EDLP 345
            P+ +      A  ++   DG +   +   +  D   T  + S      +E     + L 
Sbjct: 326 NPRRL---SIIAESIR---DGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL- 378

Query: 346 SNADFDEEVDIARKVLNKL------TSTTGSLPSLSDDSALVKGNKEQDS---DKTVNES 396
             + F     I   +L+ +      +     +  L   S + K  KE         +   
Sbjct: 379 --SVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELK 436

Query: 397 AKVSDVSKLN----SSKSKPKSLKQ-TEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGE 451
            K+ +   L+       + PK+          L    +  ++   L N E  +R + F  
Sbjct: 437 VKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFY-SHIGHHLKNIEHPERMTLFRM 495

Query: 452 V-VSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
           V + F               FL+ K +   + A +AS           G  L  L+ L  
Sbjct: 496 VFLDF--------------RFLEQK-IRHDSTAWNAS-----------GSILNTLQQLKF 529

Query: 511 KLAHDKEIDKSKNETNDHR--------------NLYLAKEGLILEGT--PAAEGVSDDDM 554
              +   I    N+    R              NL  +K   +L        E + ++  
Sbjct: 530 YKPY---I--CDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEE-- 582

Query: 555 SKRQM 559
           + +Q+
Sbjct: 583 AHKQV 587

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 57.6 bits (138), Expect = 1e-08
 Identities = 73/383 (19%), Positives = 121/383 (31%), Gaps = 121/383 (31%)

Query: 328 DAETASDDSNSSEKEDLPSN-----ADFD-EEV-DIARKVLNKLTSTTGSLPSLSDDSAL 380
           D ET         K+ L         +FD ++V D+ + +L+K                 
Sbjct: 8   DFETGEHQY--QYKDILSVFEDAFVDNFDCKDVQDMPKSILSK----------------- 48

Query: 381 VKGNKEQDSDKTVNESAKVSDVSKL-NSSKSKPKSLKQTEGEDELQ-NTIFI-------C 431
                 ++ D  +     VS   +L  +  SK + + Q   E+ L+ N  F+        
Sbjct: 49  ------EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQ 102

Query: 432 NLPFDLDNEEVKQRFSAFGEVVSF----VPVLHQVTK--------RP---------KGTG 470
             P  +    ++QR   + +   F    V  L    K        RP          G+G
Sbjct: 103 RQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSG 162

Query: 471 FLKFKTVEAATAAVSAS-KTTSGLGIF-LK-GRQLT---VLKALDKKLAHDKEIDKSKNE 524
               KT  A    +S   +      IF L      +   VL+ L +KL +   ID +   
Sbjct: 163 ----KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEML-QKLLYQ--IDPNWTS 215

Query: 525 TNDH-RNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTK----LQSPNFHVSRTR 579
            +DH  N+ L    +  E               R++L  K        L     +V   +
Sbjct: 216 RSDHSSNIKLRIHSIQAE--------------LRRLLKSKPYENCLLVLL----NVQNAK 257

Query: 580 LV-IYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAF 638
               +NL         K L    + +R    K V     FL +     +   H+S     
Sbjct: 258 AWNAFNL-------SCKIL----LTTR---FKQVTD---FLSAATTTHISLDHHSMT--- 297

Query: 639 VEFTEHQHALVALRVLNNNPSKL 661
              T  +   + L+ L+  P  L
Sbjct: 298 --LTPDEVKSLLLKYLDCRPQDL 318

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 50.2 bits (119), Expect = 2e-06
 Identities = 62/478 (12%), Positives = 130/478 (27%), Gaps = 124/478 (25%)

Query: 211 GSKTQKWKLIIRNI--PFKA--KVNEIKDMFSPV---GLVWNVYIPHNTDTGLSKGFAFV 263
           G    ++K I+      F       +++DM   +     + ++ +  +  +G        
Sbjct: 12  GEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGT-----LR 66

Query: 264 KFTCKRD-AESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDD 322
            F       E  +QKF           V+  +  N Y    +    + +           
Sbjct: 67  LFWTLLSKQEEMVQKF-----------VEEVLRIN-YKFLMSPIKTEQR-----QPSMMT 109

Query: 323 DLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTT--------GS---- 370
            +  +  +   +D+    K ++       +     R+ L +L            GS    
Sbjct: 110 RMYIEQRDRLYNDNQVFAKYNVSR----LQPYLKLRQALLELRPAKNVLIDGVLGSGKTW 165

Query: 371 --LPSLSDDSALVK----------GNKEQDSD---KTVNESAKVSDVSKLNSSKSKPKSL 415
             L          K           N                ++       S  S    L
Sbjct: 166 VALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL 225

Query: 416 KQTEGEDELQNTIFICNLPF-----DLDNEEVKQRFSAFG------------EVVSFVPV 458
           +    + EL+    + + P+      L N +  + ++AF             +V  F+  
Sbjct: 226 RIHSIQAELRR--LLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSA 283

Query: 459 LH--QVTKRPKGTGFLKFKTVE--AATAAVSASK------TTSGLGIFLKGRQLTVLKA- 507
                ++           +                     TT+   + +    +    A 
Sbjct: 284 ATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT 343

Query: 508 LD--KKLAHDK---EIDKSKN--ETNDHRNLY--LAKEGLIL-EGT--PAA-------EG 548
            D  K +  DK    I+ S N  E  ++R ++  L+    +       P         + 
Sbjct: 344 WDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS----VFPPSAHIPTILLSLIWFDV 399

Query: 549 VSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNL-----PKSMTEKGLKKLCIDA 601
           +  D M     LH+  + + Q     +S     I ++      K   E  L +  +D 
Sbjct: 400 IKSDVMVVVNKLHKYSLVEKQPKESTIS-----IPSIYLELKVKLENEYALHRSIVDH 452

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 51.6 bits (124), Expect = 1e-08
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 11/86 (12%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           ++F+   P  +D+ ++ + F AFG V S V     + K       ++   V A  A +S 
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVV-----MDKDKGVFAIVEMGDVGAREAVLSQ 64

Query: 487 SKTTSGLGIFLKGRQLTVLKALDKKL 512
           S+ +      L G +L V     K+ 
Sbjct: 65  SQHS------LGGHRLRVRPREQKEF 84

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 16/96 (16%), Positives = 31/96 (32%), Gaps = 7/96 (7%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G  GS   +  + +   P      ++ + F   G V +V +  +        FA V+   
Sbjct: 1   GSSGSSGLR-SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGD 54

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGG 303
               E+ + + +    G   + V     K   S   
Sbjct: 55  VGAREAVLSQ-SQHSLGGHRLRVRPREQKEFQSPAS 89

>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} Length = 89

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 12/97 (12%)

Query: 415 LKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKF 474
           ++ +       + +F+     D+  EE++Q F  +GEVV        + K  +   F+ F
Sbjct: 1   MRGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVF-----IPKPFRAFAFVTF 55

Query: 475 KTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
              + A +              +KG  + +  A  K 
Sbjct: 56  ADDKVAQSLCGEDLI-------IKGISVHISNAEPKH 85

>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} Length = 89

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 19/90 (21%), Positives = 32/90 (35%), Gaps = 7/90 (7%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G         K+ +          E++  F   G V +V+IP        + FAFV F  
Sbjct: 3   GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFAD 57

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKN 297
            + A+S   +          + +  A PK+
Sbjct: 58  DKVAQSLCGE--DLIIKGISVHISNAEPKH 85

>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 Length = 88

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 12/84 (14%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +F+     D+  +E+++ FS +G+V+        + K  +   F+ F   + A +     
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMD-----VFIPKPFRAFAFVTFADDQIAQSLCGED 62

Query: 488 KTTSGLGIFLKGRQLTVLKALDKK 511
                    +KG  + +  A  K 
Sbjct: 63  LI-------IKGISVHISNAEPKH 79

>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 Length = 88

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 22/95 (23%), Positives = 39/95 (41%), Gaps = 8/95 (8%)

Query: 211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRD 270
           GS      + +         +E+++ FS  G V +V+IP        + FAFV F   + 
Sbjct: 1   GSSGSS-GVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQI 54

Query: 271 AESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAA 305
           A+S              + +  A PK+  +SG ++
Sbjct: 55  AQSLCG--EDLIIKGISVHISNAEPKHNSNSGPSS 87

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 52.9 bits (126), Expect = 4e-08
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           + I+  P  A +++IK+     G V N+ +         KG  FV F     A+  ++  
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETP 170

Query: 279 NGQKFGKRPIAVDWA 293
            GQK+ +  + + + 
Sbjct: 171 -GQKYKETDLLILFK 184

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 51.0 bits (121), Expect = 2e-07
 Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 7/85 (8%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
             +++I   P D   +++K+     G+V++ + +   + K  KG+ F+ F ++E+A   V
Sbjct: 109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKFV 167

Query: 485 SASKTTSGLGIFLKGRQLTVLKALD 509
                        K   L +L   D
Sbjct: 168 ETPGQK------YKETDLLILFKDD 186

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 49.9 bits (119), Expect = 9e-08
 Identities = 16/93 (17%), Positives = 39/93 (41%), Gaps = 11/93 (11%)

Query: 219 LIIRN--IPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           L++ N  +      N++  +    GLV  + +P N      K ++F ++    +++ A  
Sbjct: 28  LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYV 81

Query: 277 KFNGQKFGK---RPIAVDWAVPKNIYSSGGAAA 306
             NG++      + I +     + +  SG ++ 
Sbjct: 82  TLNGKEVVDDLGQKITLYLNFVEKVQWSGPSSG 114

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 45.7 bits (108), Expect = 3e-06
 Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 10/85 (11%)

Query: 406 NSSKSKPKSLKQTEGE--DELQNTIFICN--LPFDLDNEEVKQRFSAFGEVVSFVPVLHQ 461
            SS +K   L+    E       ++ + N  L   +   ++       G V + +   + 
Sbjct: 4   GSSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN- 62

Query: 462 VTKRPKGTGFLKFKTVEAATAAVSA 486
                K   F +++T E +  A   
Sbjct: 63  -----KPYSFARYRTTEESKRAYVT 82

>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* Length = 437

 Score = 52.9 bits (126), Expect = 2e-07
 Identities = 20/125 (16%), Positives = 50/125 (40%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L +  + +    ++++  F   G +  +++ ++  +G  +G+AF+++  +RD  SA +  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 279 NGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNS 338
           +G+K   R + VD    + +        G    G     +  +      D  +  D+   
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPG 224

Query: 339 SEKED 343
                
Sbjct: 225 PSPLP 229

>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* Length = 437

 Score = 52.2 bits (124), Expect = 4e-07
 Identities = 10/58 (17%), Positives = 29/58 (50%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAA 483
            T+F+  + +D    ++++ F  +G +     V  + + +P+G  F++++      +A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160

>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 Length = 112

 Score = 47.6 bits (113), Expect = 5e-07
 Identities = 22/103 (21%), Positives = 45/103 (43%), Gaps = 10/103 (9%)

Query: 403 SKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFD-LDNEEVKQRFSAFGEVVSFVPVLHQ 461
           S  +  K + K  ++ + + EL   I + NLP     +  V +    +G++ +++ +   
Sbjct: 3   SGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM--- 59

Query: 462 VTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV 504
              R K   F++ +T E A A V          ++ +GR + V
Sbjct: 60  ---RMKSQAFIEMETREDAMAMVDHCLKK---ALWFQGRCVKV 96

>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 Length = 112

 Score = 47.8 bits (114), Expect = 5e-07
 Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 4/76 (5%)

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
            +++   S  G +  + +          G A V F    +A+  IQ  +G+ FG R I  
Sbjct: 41  EDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 96

Query: 291 DWAVPKNIYSSGGAAA 306
                   Y SG ++ 
Sbjct: 97  QAWDGTTDYQSGPSSG 112

>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 Length = 104

 Score = 47.2 bits (112), Expect = 7e-07
 Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 232 EIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD 291
              +M    G V  + +  N    L  G  +VKF  + DAE A+   N + F  +PI  +
Sbjct: 43  VFTEMEEKYGEVEEMNVCDNLGDHL-VGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

Query: 292 W 292
            
Sbjct: 102 L 102

>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 Length = 104

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 21/99 (21%), Positives = 33/99 (33%), Gaps = 16/99 (16%)

Query: 408 SKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSA-FGEVVSFVPVLHQVTKRP 466
           S      L+    + E+Q         +D   EEV       +GEV     V   +    
Sbjct: 16  SSQSADGLRSAVSDVEMQEH-------YDEFFEEVFTEMEEKYGEVEEMN-VCDNLGDHL 67

Query: 467 KGTGFLKFKTVEAATAAVSASKTTSGL-GIFLKGRQLTV 504
            G  ++KF+  E A  AV        L   +  G+ +  
Sbjct: 68  VGNVYVKFRREEDAEKAVID------LNNRWFNGQPIHA 100

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 46.9 bits (111), Expect = 9e-07
 Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 3/85 (3%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQ--VTKRPKGTGFLKFKTVEAATAA 483
             +F+  LP D+D +E+   F  FG +V   P   +      PKG  FL F+   +  A 
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68

Query: 484 VSASKTTSG-LGIFLKGRQLTVLKA 507
           + A     G L + +    +     
Sbjct: 69  IDACLEEDGKLYLCVSSPTIKDKPV 93

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 46.7 bits (111), Expect = 1e-06
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 226 FKAKVNEIKDMFSPVGLVWNVYIPHNTD--TGLSKGFAFVKFTCKRDAESAIQKFNGQKF 283
           ++  V +++D  S  GLV ++ IP   D       G  FV+FT   D + A+Q   G+KF
Sbjct: 25  YEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF 84

Query: 284 GKRPIAVDWAVPKNIYSSG 302
             R +   +    + Y   
Sbjct: 85  ANRVVVTKY-CDPDSYHRR 102

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 12/60 (20%), Positives = 27/60 (45%), Gaps = 4/60 (6%)

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
           +++ +  +  G V ++Y+  N+  G      +VK      A +A+   +G+ F  + I  
Sbjct: 32  DDVIEECNKHGGVIHIYVDKNSAQG----NVYVKCPSIAAAIAAVNALHGRWFAGKMITA 87

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 46.6 bits (110), Expect = 3e-06
 Identities = 22/99 (22%), Positives = 39/99 (39%), Gaps = 7/99 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           I + NL + +  + + Q FS FG V+  +      TK  +    L++    +A  A  + 
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALLQYADPVSAQHAKLSL 104

Query: 488 KTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETN 526
               G  I+     L +  +    L      DKS++ T 
Sbjct: 105 D---GQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTR 140

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 45.1 bits (106), Expect = 1e-05
 Identities = 12/82 (14%), Positives = 34/82 (41%), Gaps = 6/82 (7%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           +I+ N+ +   ++ +  +FS  G V  +          ++  A +++     A+ A    
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 104

Query: 279 NGQKF--GKRPIAVDWAVPKNI 298
           +GQ        + +D++   ++
Sbjct: 105 DGQNIYNACCTLRIDFSKLTSL 126

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 45.0 bits (106), Expect = 7e-06
 Identities = 22/99 (22%), Positives = 39/99 (39%), Gaps = 7/99 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           I + NL + +  + + Q FS FG V+  +      TK  +    L++    +A  A  + 
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALLQYADPVSAQHAKLSL 86

Query: 488 KTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETN 526
               G  I+     L +  +    L      DKS++ T 
Sbjct: 87  D---GQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTR 122

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 44.6 bits (105), Expect = 9e-06
 Identities = 12/82 (14%), Positives = 34/82 (41%), Gaps = 6/82 (7%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           +I+ N+ +   ++ +  +FS  G V  +          ++  A +++     A+ A    
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 86

Query: 279 NGQKF--GKRPIAVDWAVPKNI 298
           +GQ        + +D++   ++
Sbjct: 87  DGQNIYNACCTLRIDFSKLTSL 108

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 44.3 bits (104), Expect = 1e-05
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 7/82 (8%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L I+N  +   V+ +  + +PVG V  + I            A V+F     A+ A    
Sbjct: 28  LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGI-----QAMVEFESVLCAQKAKAAL 82

Query: 279 NGQKF--GKRPIAVDWAVPKNI 298
           NG     G   + +++A P  +
Sbjct: 83  NGADIYAGCCTLKIEYARPTRL 104

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 43.9 bits (103), Expect = 1e-05
 Identities = 22/124 (17%), Positives = 45/124 (36%), Gaps = 11/124 (8%)

Query: 406 NSSKSKPKSLKQTEGEDELQNT---IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQV 462
           + S  K  +      +    N    + I N  + +  + +    +  G+V   V     +
Sbjct: 3   SGSSGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIV-----I 57

Query: 463 TKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSK 522
            KR      ++F++V  A  A +A    +G  I+     L +  A   +L   +  + S 
Sbjct: 58  FKRNGIQAMVEFESVLCAQKAKAA---LNGADIYAGCCTLKIEYARPTRLNVIRNDNDSW 114

Query: 523 NETN 526
           + T 
Sbjct: 115 DYTK 118

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 45.5 bits (107), Expect = 2e-05
 Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 6/76 (7%)

Query: 222 RNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQ 281
           +++      + I+ +FS +G +  +    +      K   FVKF  + +AE A +  + Q
Sbjct: 149 KHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQ 202

Query: 282 KFGKRPIAVDWAVPKN 297
                         + 
Sbjct: 203 TLLLPSDKEWDDRREG 218

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118

 Score = 42.8 bits (101), Expect = 3e-05
 Identities = 15/63 (23%), Positives = 22/63 (34%), Gaps = 4/63 (6%)

Query: 232 EIKDMFSPVGLVWNVYIPHNTDTGL----SKGFAFVKFTCKRDAESAIQKFNGQKFGKRP 287
           E+ +     G V  V I                 FV+F+   +   AIQ  NG+ F  R 
Sbjct: 41  EVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRK 100

Query: 288 IAV 290
           +  
Sbjct: 101 VVA 103

>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 Length = 102

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 10/79 (12%)

Query: 427 TIFICNLPFDLDNE-EVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
            + I +     +   ++ Q    FG + + + +            F++  T E A AAV 
Sbjct: 17  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL------NKINEAFIEMATTEDAQAAVD 70

Query: 486 ASKTTSGLGIFLKGRQLTV 504
              TT      + G+ + V
Sbjct: 71  YYTTTP---ALVFGKPVRV 86

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 39.4 bits (92), Expect = 4e-04
 Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 1/61 (1%)

Query: 232 EIKDMFSPVGLVWNVYIPHNTDTG-LSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
           E K+     G V    I              F++F     A  A+   NG+ FG R +  
Sbjct: 29  ETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKA 88

Query: 291 D 291
            
Sbjct: 89  C 89

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 38.8 bits (90), Expect = 5e-04
 Identities = 18/97 (18%), Positives = 33/97 (34%), Gaps = 19/97 (19%)

Query: 419 EGEDELQNTIFICNLPFDLDNEEVKQRF-----SAFGEVVSFVPVLHQVTKRPKGTGFLK 473
                    + +  LP  + +E +   F     S  G V+S+        +R    G L 
Sbjct: 2   SSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLT 53

Query: 474 FKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
           F+    A   ++ +         L G QL++  A  +
Sbjct: 54  FREPADAERVLAQADHE------LHGAQLSLRPAPPR 84

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	676
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.98
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.97
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.97
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.97
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.97
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.97
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.96
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.96
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.96
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.96
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.96
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.96
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.95
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.95
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.95
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.95
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.95
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.94
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.94
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.94
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.94
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.93
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.93
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.83
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.83
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.81
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.8
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.79
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.78
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.78
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.77
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.74
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.74
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.72
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.71
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.71
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.71
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.71
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.7
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.7
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.69
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.69
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.69
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.69
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.69
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.69
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.69
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.68
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.68
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.68
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.68
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.67
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.67
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.67
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.67
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.67
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.67
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.67
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.67
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.67
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.67
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.67
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.67
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.67
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.67
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.66
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.66
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.66
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.66
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.66
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.66
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.66
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.66
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.66
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.66
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.66
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.66
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.66
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.66
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.66
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.66
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.66
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.66
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.66
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.65
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.65
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.65
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.65
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.65
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.65
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.65
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.65
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.65
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.65
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.65
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.65
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.65
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.65
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.65
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.65
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.65
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.65
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.64
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.64
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.64
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.64
2div_A	99	TRNA selenocysteine associated protein; structural	99.64
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.64
2div_A	99	TRNA selenocysteine associated protein; structural	99.64
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.64
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.64
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.64
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.64
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.64
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.64
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.64
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.64
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.64
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.63
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.63
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.63
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.63
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.63
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.63
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.63
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.63
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.63
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.63
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.63
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.63
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.63
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.63
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.63
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.63
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.63
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.63
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.63
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.63
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.63
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.63
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.63
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.63
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.62
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.62
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.62
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.62
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.62
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.62
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.62
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.62
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.62
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.62
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.62
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.62
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.62
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.62
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.62
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.62
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.62
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.62
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.62
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.62
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.61
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.61
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.61
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.61
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.61
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.61
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.61
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.61
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.61
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.61
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.61
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.61
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.61
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.61
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.61
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.61
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.61
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.61
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.61
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.6
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.6
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.6
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.6
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.6
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.6
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.6
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.6
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.6
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.6
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.6
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.6
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.6
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.6
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.6
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.6
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.6
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.6
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.6
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.59
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.59
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.59
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.59
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.59
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.59
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.59
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.59
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.59
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.59
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.59
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.59
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.59
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.59
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.59
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.58
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.58
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.58
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.58
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.58
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.58
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.58
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.58
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.58
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.58
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.57
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.57
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.57
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.57
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.57
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.57
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.57
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.57
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.57
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.57
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.57
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.57
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.57
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.56
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.56
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.56
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.56
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.56
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.56
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.56
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.56
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.56
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.56
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.55
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.55
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.55
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.55
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.55
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.55
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.55
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.55
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.55
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.55
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.55
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.55
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.55
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.55
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.55
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.55
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.54
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.54
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.54
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.54
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.54
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.54
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.54
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.53
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.53
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.29
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.53
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.53
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.53
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.53
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.53
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.53
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.52
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.52
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.52
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.52
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.52
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.52
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.52
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.52
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.52
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.52
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.51
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.51
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.51
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.51
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.51
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.51
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.51
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.26
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.51
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.51
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.5
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.5
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.5
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.5
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.5
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.49
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.49
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.49
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.49
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.49
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.49
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.49
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.49
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.48
1x5p_A	97	Negative elongation factor E; structure genomics,	99.48
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.48
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.48
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.48
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.48
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.48
1x5p_A	97	Negative elongation factor E; structure genomics,	99.48
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.48
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.48
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.47
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.47
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.46
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.46
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.46
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.46
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.44
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.44
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.44
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.44
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.44
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.43
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.42
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.41
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.4
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.4
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.39
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.39
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.38
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.38
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.35
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.35
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.33
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.33
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.32
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.3
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.26
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.26
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.26
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.16
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.15
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.13
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.13
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.07
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.05
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.93
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.87
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.82
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.8
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.65
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.59
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.54
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.49
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.37
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.07
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.7
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.68
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.42
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.41
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.32
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.08
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.84
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.84
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.61
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.51
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.35
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.25
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.89
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.72
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.16
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	93.71
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.85
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.37
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	81.01

>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

Probab=100.00  E-value=5.7e-42  Score=351.83  Aligned_cols=249  Identities=20%  Similarity=0.263  Sum_probs=225.7

Q ss_pred             cccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCee
Q 005812          118 QRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEI  197 (676)
Q Consensus       118 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~  197 (676)
                      ....++|||+|||+++++++|+++|+.|| |.++.+               ++++|||||+|.+.++|.+|+..|||..+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~---------------~~~~g~afV~f~~~~~A~~A~~~l~~~~~   82 (284)
T 3smz_A           19 FRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV---------------DKYKGTAFVTLLNGEQAEAAINAFHQSRL   82 (284)
T ss_dssp             HHCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE---------------ETTTTEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE---------------ecCCCEEEEEeCCHHHHHHHHHHcCCCee
Confidence            34668999999999999999999999999 999884               46789999999999999999999999999


Q ss_pred             cCeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHH
Q 005812          198 KGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK  277 (676)
Q Consensus       198 ~~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~  277 (676)
                      .|+.|.+...      ...++|||+|||+.+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+|+..
T Consensus        83 ~g~~i~v~~~------~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~  156 (284)
T 3smz_A           83 RERELSVQLQ------PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD  156 (284)
T ss_dssp             TTEECEEEEC------CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCeEEEEEec------CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHH
Confidence            9999999753      3567999999999999999999999999999999999988999999999999999999999999


Q ss_pred             hCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHH
Q 005812          278 FNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIA  357 (676)
Q Consensus       278 l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  357 (676)
                      |+|..+.|+.|.|.|+.+.....                                                         
T Consensus       157 l~~~~~~g~~i~v~~a~~~~~~~---------------------------------------------------------  179 (284)
T 3smz_A          157 LLGKPLGPRTLYVHWTDAGQLTP---------------------------------------------------------  179 (284)
T ss_dssp             HTTCEETTEECEEEECCGGGCCT---------------------------------------------------------
T ss_pred             hCCCEeCCcEEEEEECCCCCCCc---------------------------------------------------------
Confidence            99999999999999986542100                                                         


Q ss_pred             HHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCC
Q 005812          358 RKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDL  437 (676)
Q Consensus       358 ~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~  437 (676)
                                                                                     .....++|||+|||+.+
T Consensus       180 ---------------------------------------------------------------~~~~~~~l~v~nlp~~~  196 (284)
T 3smz_A          180 ---------------------------------------------------------------ALLHSRCLCVDRLPPGF  196 (284)
T ss_dssp             ---------------------------------------------------------------TTTSCSEEEEECCCTTC
T ss_pred             ---------------------------------------------------------------ccCCccEEEEecCCccc
Confidence                                                                           11124799999999995


Q ss_pred             -CHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhh
Q 005812          438 -DNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAH  514 (676)
Q Consensus       438 -teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~  514 (676)
                       ++++|+++|+.||.|.++.|+.+. +|.++|+|||+|.+.++|.+|+..||     |..|+|++|.|.|+.++....
T Consensus       197 ~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~l~v~~a~~~~~~~  268 (284)
T 3smz_A          197 NDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQAD-----GLSLGGSHLRVSFCAPGPPGR  268 (284)
T ss_dssp             CCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHT-----TCEETTEECEEEECCSSSCHH
T ss_pred             CCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhC-----CCccCCeEEEEEEecCCCccc
Confidence             999999999999999999998885 78999999999999999999999999     999999999999999887543

>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

Probab=100.00  E-value=7.6e-42  Score=352.40  Aligned_cols=253  Identities=19%  Similarity=0.273  Sum_probs=214.2

Q ss_pred             hhcccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCC
Q 005812          116 QKQRVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQK  195 (676)
Q Consensus       116 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~  195 (676)
                      ...+..++|||+|||+++++++|+++|+.||.|.+|.++.++.           .++|||||+|.+.++|.+|+. +|+.
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----------~~~g~afV~f~~~~~A~~A~~-~~~~  103 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-----------KNFRFARIEFARYDGALAAIT-KTHK  103 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------SSSEEEEEEESSHHHHHHHHT-TTTC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC-----------CCcEEEEEEECCHHHHHHHHH-hCCc
Confidence            3456788999999999999999999999999999999886542           258999999999999999995 9999


Q ss_pred             eecCeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCC-ceEEEEEcccCCCCCceeEEEEEecCHHHHHHH
Q 005812          196 EIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVG-LVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA  274 (676)
Q Consensus       196 ~~~~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G-~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A  274 (676)
                      .+.|+.|.+...       ..++|||+|||+.+++++|+++|+.|| .|..|.++.+.. |.++|||||+|.+.++|.+|
T Consensus       104 ~~~g~~i~v~~~-------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A  175 (292)
T 2ghp_A          104 VVGQNEIIVSHL-------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYC  175 (292)
T ss_dssp             EETTEECEEEEC-------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHH
T ss_pred             EeCCcEEEEEEC-------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHH
Confidence            999999999643       578999999999999999999999999 999999998864 77999999999999999999


Q ss_pred             HHHhCCceeCCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHH
Q 005812          275 IQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEV  354 (676)
Q Consensus       275 ~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  354 (676)
                      +..|+|..+.|+.|.|.|+.+.......                                                    
T Consensus       176 ~~~l~g~~~~g~~l~v~~a~~~~~~~~~----------------------------------------------------  203 (292)
T 2ghp_A          176 VEKLNGLKIEGYTLVTKVSNPLEKSKRT----------------------------------------------------  203 (292)
T ss_dssp             HHHHTTCEETTEECEEEECCCC----------------------------------------------------------
T ss_pred             HHHhCCCEeCCcEEEEEECCCCcccccc----------------------------------------------------
Confidence            9999999999999999999765321000                                                    


Q ss_pred             HHHHHHhhcccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCC
Q 005812          355 DIARKVLNKLTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLP  434 (676)
Q Consensus       355 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp  434 (676)
                                                                                      ......+++|||+|||
T Consensus       204 ----------------------------------------------------------------~~~~~~~~~l~v~nlp  219 (292)
T 2ghp_A          204 ----------------------------------------------------------------DSATLEGREIMIRNLS  219 (292)
T ss_dssp             -------------------------------------------------------------------CCTTTEEEEEEEC
T ss_pred             ----------------------------------------------------------------cccCCCCceEEEECCC
Confidence                                                                            0011235799999999


Q ss_pred             CC-CCHHHHHHHHHhCCceeEEEEeecCC-CCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCc
Q 005812          435 FD-LDNEEVKQRFSAFGEVVSFVPVLHQV-TKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK  510 (676)
Q Consensus       435 ~~-~teedl~~~F~~~G~v~~v~i~~~~~-~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k  510 (676)
                      +. +++++|+++|+.||.|..|+++.+.. ++.++|||||+|.+.++|.+|+ .||     |..|+|++|.|.||.+|
T Consensus       220 ~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~-----g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          220 TELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMN-----RSLLGNREISVSLADKK  291 (292)
T ss_dssp             TTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGT-----TEEETTEEEEEEECCCC
T ss_pred             cccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-Hhc-----CCEECCcEEEEEEecCC
Confidence            99 99999999999999999999988765 5899999999999999999999 999     99999999999999876

>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

Probab=100.00  E-value=6.1e-40  Score=336.74  Aligned_cols=243  Identities=20%  Similarity=0.240  Sum_probs=215.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++|||+|||.++++++|+++|+.|| |.+|.+.      +++|||||+|.+.++|.+|+..|+|..+.|+.|.|.|+.
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~~------~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~   93 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD------KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP   93 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEEE------TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEEe------cCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC
Confidence            567999999999999999999999999 9999883      378999999999999999999999999999999999853


Q ss_pred             CCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCC
Q 005812          295 PKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSL  374 (676)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  374 (676)
                      +                                                                               
T Consensus        94 ~-------------------------------------------------------------------------------   94 (284)
T 3smz_A           94 T-------------------------------------------------------------------------------   94 (284)
T ss_dssp             C-------------------------------------------------------------------------------
T ss_pred             C-------------------------------------------------------------------------------
Confidence            2                                                                               


Q ss_pred             CCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE
Q 005812          375 SDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS  454 (676)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~  454 (676)
                                                                        .++|||+|||+.+++++|+++|+.||.|..
T Consensus        95 --------------------------------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~  124 (284)
T 3smz_A           95 --------------------------------------------------DALLCVANLPPSLTQQQFEELVRPFGSLER  124 (284)
T ss_dssp             --------------------------------------------------SCEEEEESCCTTCCHHHHHHHHGGGSCEEE
T ss_pred             --------------------------------------------------CCEEEEcCCCCcCCHHHHHHHHHhcCCeeE
Confidence                                                              258999999999999999999999999999


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhhhHhhhhhcccccccCccccc
Q 005812          455 FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLA  534 (676)
Q Consensus       455 v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~  534 (676)
                      ++++.+..+|.++|||||+|.+.++|.+|+..|+     |..++|+.|.|.++.++....                    
T Consensus       125 ~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-----~~~~~g~~i~v~~a~~~~~~~--------------------  179 (284)
T 3smz_A          125 CFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL-----GKPLGPRTLYVHWTDAGQLTP--------------------  179 (284)
T ss_dssp             EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-----TCEETTEECEEEECCGGGCCT--------------------
T ss_pred             EEEEeeCCCCccceEEEEEECCHHHHHHHHHHhC-----CCEeCCcEEEEEECCCCCCCc--------------------
Confidence            9999998899999999999999999999999999     999999999999987642110                    


Q ss_pred             ccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCeEEEecCCccc-CHHHHHHHHHHHHHhhhcccCCCc
Q 005812          535 KEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKSM-TEKGLKKLCIDAVVSRASKQKPVI  613 (676)
Q Consensus       535 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~V~nlp~~~-te~~l~~~F~~~~~~~~~~~~G~V  613 (676)
                                                            .....++|||+|||..+ |+++|+++|+         .||.|
T Consensus       180 --------------------------------------~~~~~~~l~v~nlp~~~~~~~~l~~~f~---------~~G~i  212 (284)
T 3smz_A          180 --------------------------------------ALLHSRCLCVDRLPPGFNDVDALCRALS---------AVHSP  212 (284)
T ss_dssp             --------------------------------------TTTSCSEEEEECCCTTCCCHHHHHHHTC---------SSSCC
T ss_pred             --------------------------------------ccCCccEEEEecCCcccCCHHHHHHHhh---------CCCCe
Confidence                                                  00134789999999995 9999999999         69999


Q ss_pred             eEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCCCCCcccCccccccccc
Q 005812          614 KQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAADAQCK  675 (676)
Q Consensus       614 ~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~~~~~~~~~~~~~~~~~  675 (676)
                      .+|+|++++ +      +.++|+|||+|.++++|.+|+..|||..+   ..+++.|.+|..+
T Consensus       213 ~~v~i~~~~-~------g~~~g~afV~f~~~~~A~~A~~~l~g~~~---~g~~l~v~~a~~~  264 (284)
T 3smz_A          213 TFCQLACGQ-D------GQLKGFAVLEYETAEMAEEAQQQADGLSL---GGSHLRVSFCAPG  264 (284)
T ss_dssp             SEEEEEECS-S------CCEEEEEEEECSSHHHHHHHHHHHTTCEE---TTEECEEEECCSS
T ss_pred             EEEEEEECC-C------CCcccEEEEEeCCHHHHHHHHHHhCCCcc---CCeEEEEEEecCC
Confidence            999999885 2      58899999999999999999999999754   3367788887654

>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

Probab=100.00  E-value=1.9e-39  Score=334.43  Aligned_cols=252  Identities=17%  Similarity=0.222  Sum_probs=210.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+++++++|+++|+.||.|.+|.|+++...  ++|||||+|.+.++|.+|++ ++|..+.|+.|.|.
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~  113 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVS  113 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEE
Confidence            3456789999999999999999999999999999999997633  57999999999999999996 89999999999999


Q ss_pred             EecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCC
Q 005812          292 WAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSL  371 (676)
Q Consensus       292 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  371 (676)
                      ++.                                                                             
T Consensus       114 ~~~-----------------------------------------------------------------------------  116 (292)
T 2ghp_A          114 HLT-----------------------------------------------------------------------------  116 (292)
T ss_dssp             ECC-----------------------------------------------------------------------------
T ss_pred             ECC-----------------------------------------------------------------------------
Confidence            852                                                                             


Q ss_pred             CCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCC-
Q 005812          372 PSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFG-  450 (676)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G-  450 (676)
                                                                           .++|||+|||+.+++++|+++|+.|| 
T Consensus       117 -----------------------------------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~  143 (292)
T 2ghp_A          117 -----------------------------------------------------ECTLWMTNFPPSYTQRNIRDLLQDINV  143 (292)
T ss_dssp             -----------------------------------------------------SCEEEEECCCTTCCHHHHHHHHHHTTC
T ss_pred             -----------------------------------------------------CCEEEEECCCCCCCHHHHHHHHHHhCC
Confidence                                                                 26899999999999999999999999 


Q ss_pred             ceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhhhHhhhhhcccccccCc
Q 005812          451 EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRN  530 (676)
Q Consensus       451 ~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~  530 (676)
                      .|..|.++.+.. +.++|||||+|.+.++|.+|+..|+     |..|+|+.|.|.++.++......              
T Consensus       144 ~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l~v~~a~~~~~~~~~--------------  203 (292)
T 2ghp_A          144 VALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLN-----GLKIEGYTLVTKVSNPLEKSKRT--------------  203 (292)
T ss_dssp             CCCEEECC--------CCEEEEECSSHHHHHHHHHHHT-----TCEETTEECEEEECCCC--------------------
T ss_pred             CeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhC-----CCEeCCcEEEEEECCCCcccccc--------------
Confidence            999999988764 7889999999999999999999999     99999999999998865422100              


Q ss_pred             ccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCeEEEecCCcc-cCHHHHHHHHHHHHHhhhccc
Q 005812          531 LYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTRLVIYNLPKS-MTEKGLKKLCIDAVVSRASKQ  609 (676)
Q Consensus       531 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~V~nlp~~-~te~~l~~~F~~~~~~~~~~~  609 (676)
                                                              .......++|||+|||.. +|+++|+++|+         .
T Consensus       204 ----------------------------------------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~---------~  234 (292)
T 2ghp_A          204 ----------------------------------------DSATLEGREIMIRNLSTELLDENLLRESFE---------G  234 (292)
T ss_dssp             -------------------------------------------CCTTTEEEEEEECTTTCCHHHHHHHHG---------G
T ss_pred             ----------------------------------------cccCCCCceEEEECCCcccCCHHHHHHHHh---------c
Confidence                                                    000113478999999999 99999999999         6


Q ss_pred             CCCceEeeeeeccc-cCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCCCCCcccCccccccccc
Q 005812          610 KPVIKQIKFLQSLK-KGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPSKLFYHHCFDAADAQCK  675 (676)
Q Consensus       610 ~G~V~~v~i~~~~~-~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~~~~~~~~~~~~~~~~~  675 (676)
                      ||.|..|+++++.. +      +.++|+|||+|.++++|.+|+ .|||..+   ..+++.|.+|+.|
T Consensus       235 ~G~v~~v~i~~~~~~t------g~~~g~afV~F~~~~~A~~A~-~l~g~~~---~g~~i~V~~a~~k  291 (292)
T 2ghp_A          235 FGSIEKINIPAGQKEH------SFNNCCAFMVFENKDSAERAL-QMNRSLL---GNREISVSLADKK  291 (292)
T ss_dssp             GSCEEEEECCSCCC---------CCCEEEEEEESSHHHHHHHG-GGTTEEE---TTEEEEEEECCCC
T ss_pred             cCCeeEEEEEecCCcC------CCCceEEEEEeCCHHHHHHHH-HhcCCEE---CCcEEEEEEecCC
Confidence            99999999998754 2      488999999999999999999 9999743   2488889998876

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

Probab=99.98  E-value=1.3e-31  Score=262.21  Aligned_cols=173  Identities=27%  Similarity=0.410  Sum_probs=154.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ..+.++|||+|||+++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|.+|++.+++..+.|+.|++.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCC
Q 005812          293 AVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLP  372 (676)
Q Consensus       293 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  372 (676)
                      +......                                                                         
T Consensus        92 ~~~~~~~-------------------------------------------------------------------------   98 (213)
T 4f02_A           92 SQRDPSL-------------------------------------------------------------------------   98 (213)
T ss_dssp             CCCCTHH-------------------------------------------------------------------------
T ss_pred             ccccccc-------------------------------------------------------------------------
Confidence            7543210                                                                         


Q ss_pred             CCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCce
Q 005812          373 SLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEV  452 (676)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v  452 (676)
                                                                      ......+|||+|||+.+++++|+++|+.||.|
T Consensus        99 ------------------------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i  130 (213)
T 4f02_A           99 ------------------------------------------------RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNI  130 (213)
T ss_dssp             ------------------------------------------------HHHCTTEEEEESCCTTCCHHHHHHHHGGGSCE
T ss_pred             ------------------------------------------------cccccccceECCcccccHHHHHHHHHhhcCCe
Confidence                                                            00013689999999999999999999999999


Q ss_pred             eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhh
Q 005812          453 VSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLA  513 (676)
Q Consensus       453 ~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~  513 (676)
                      ..|+|+.+.  +.++|||||+|.+.++|.+|++.||     |..|+|++|.|.+|.++...
T Consensus       131 ~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~ln-----g~~~~g~~i~V~~a~~~~~~  184 (213)
T 4f02_A          131 LSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMN-----GMLLNDRKVFVGRFKSRKER  184 (213)
T ss_dssp             EEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHT-----TCEETTEECEEEECCCHHHH
T ss_pred             EEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhC-----CCEECCEEEEEEEcCCCccc
Confidence            999999885  4579999999999999999999999     99999999999999987643

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-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

Probab=99.97  E-value=1.1e-30  Score=245.74  Aligned_cols=165  Identities=27%  Similarity=0.491  Sum_probs=153.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      +.++|||+|||+++++++|+++|+.||.|.+|.++.++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.|+.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            46899999999999999999999999999999999998899999999999999999999999999999999999999986


Q ss_pred             CCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCC
Q 005812          295 PKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSL  374 (676)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  374 (676)
                      +...                                                                            
T Consensus        82 ~~~~----------------------------------------------------------------------------   85 (168)
T 1b7f_A           82 PGGE----------------------------------------------------------------------------   85 (168)
T ss_dssp             CCSS----------------------------------------------------------------------------
T ss_pred             CCcc----------------------------------------------------------------------------
Confidence            5421                                                                            


Q ss_pred             CCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE
Q 005812          375 SDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS  454 (676)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~  454 (676)
                                                                     ..+.++|||+|||..+++++|+++|++||.|..
T Consensus        86 -----------------------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~  118 (168)
T 1b7f_A           86 -----------------------------------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ  118 (168)
T ss_dssp             -----------------------------------------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEE
T ss_pred             -----------------------------------------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEE
Confidence                                                           112369999999999999999999999999999


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC--cEEEEEEc
Q 005812          455 FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG--RQLTVLKA  507 (676)
Q Consensus       455 v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g--r~l~v~~a  507 (676)
                      +.++++..++.++|||||+|.+.++|.+|+..||     |..+.|  ++|.|.||
T Consensus       119 ~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALN-----NVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-----TCCCTTCSSCCEEEEC
T ss_pred             EEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhc-----CCEecCCCeEEEEEeC
Confidence            9999998889999999999999999999999999     999988  99999986

>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

Probab=99.97  E-value=2e-30  Score=243.51  Aligned_cols=165  Identities=27%  Similarity=0.485  Sum_probs=152.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      +.++|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            35799999999999999999999999999999999998899999999999999999999999999999999999999986


Q ss_pred             CCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCC
Q 005812          295 PKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSL  374 (676)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  374 (676)
                      +...                                                                            
T Consensus        81 ~~~~----------------------------------------------------------------------------   84 (167)
T 1fxl_A           81 PSSA----------------------------------------------------------------------------   84 (167)
T ss_dssp             CCCG----------------------------------------------------------------------------
T ss_pred             CCcc----------------------------------------------------------------------------
Confidence            5421                                                                            


Q ss_pred             CCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE
Q 005812          375 SDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS  454 (676)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~  454 (676)
                                                                     ....++|||+|||..+++++|+++|++||.|..
T Consensus        85 -----------------------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~  117 (167)
T 1fxl_A           85 -----------------------------------------------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIIT  117 (167)
T ss_dssp             -----------------------------------------------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEE
T ss_pred             -----------------------------------------------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeE
Confidence                                                           011368999999999999999999999999999


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE--EEEEEc
Q 005812          455 FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ--LTVLKA  507 (676)
Q Consensus       455 v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~--l~v~~a  507 (676)
                      ++++.+..+|.++|||||+|.+.++|.+|++.||     |..|.|+.  |.|.||
T Consensus       118 ~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN-----GQKPSGATEPITVKFA  167 (167)
T ss_dssp             EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-----TCCCTTCSSCCEEEEC
T ss_pred             EEEEecCCCCCccceEEEEeCCHHHHHHHHHHhc-----CCccCCCccceEEEeC
Confidence            9999998889999999999999999999999999     99999974  888875

>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

Probab=99.97  E-value=2e-30  Score=250.44  Aligned_cols=180  Identities=19%  Similarity=0.328  Sum_probs=153.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      ......++|||+|||+++++++|+++|+.||.|.+|.|+.++.+|.++|||||+|.+.++|.+|++. ++..+.|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v   86 (196)
T 1l3k_A            8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEP   86 (196)
T ss_dssp             CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeee
Confidence            3455678999999999999999999999999999999999988999999999999999999999986 999999999999


Q ss_pred             EEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCC
Q 005812          291 DWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGS  370 (676)
Q Consensus       291 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~  370 (676)
                      .++.+......                                                                     
T Consensus        87 ~~~~~~~~~~~---------------------------------------------------------------------   97 (196)
T 1l3k_A           87 KRAVSREDSQR---------------------------------------------------------------------   97 (196)
T ss_dssp             EECCC---------------------------------------------------------------------------
T ss_pred             ecccCcccccc---------------------------------------------------------------------
Confidence            99865421000                                                                     


Q ss_pred             CCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCC
Q 005812          371 LPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFG  450 (676)
Q Consensus       371 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G  450 (676)
                                                                      .......++|||+|||+.+++++|+++|+.||
T Consensus        98 ------------------------------------------------~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G  129 (196)
T 1l3k_A           98 ------------------------------------------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG  129 (196)
T ss_dssp             -----------------------------------------------------CCSEEEEECCTTTCCHHHHHHHHTTTS
T ss_pred             ------------------------------------------------cccCCCcceEEEeCCCCCCCHHHHHHHHhcCC
Confidence                                                            00111247999999999999999999999999


Q ss_pred             ceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhh
Q 005812          451 EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAH  514 (676)
Q Consensus       451 ~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~  514 (676)
                      .|..|.++.+..++.++|||||+|.+.++|.+|+.. +     +..|+|+.|.|.+|.++....
T Consensus       130 ~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~-----~~~~~G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          130 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-K-----YHTVNGHNCEVRKALSKQEMA  187 (196)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-S-----CCEETTEECEEEECC------
T ss_pred             CeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-C-----CcEECCEEEEEEecCChhHhc
Confidence            999999999988899999999999999999999976 7     899999999999999886543

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

Probab=99.97  E-value=2.7e-30  Score=242.29  Aligned_cols=165  Identities=23%  Similarity=0.380  Sum_probs=151.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      ++|||+|||.++++++|+++|+.||.|.+|.++.++ ++.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            589999999999999999999999999999999886 5779999999999999999999999999999999999998654


Q ss_pred             CCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCC
Q 005812          297 NIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSD  376 (676)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  376 (676)
                      ...                                                                             
T Consensus        80 ~~~-----------------------------------------------------------------------------   82 (166)
T 3md3_A           80 QQS-----------------------------------------------------------------------------   82 (166)
T ss_dssp             CCC-----------------------------------------------------------------------------
T ss_pred             CCC-----------------------------------------------------------------------------
Confidence            210                                                                             


Q ss_pred             ccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEE
Q 005812          377 DSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFV  456 (676)
Q Consensus       377 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~  456 (676)
                                                                  ...+.++|||+|||+.+++++|+++|++||.|..+.
T Consensus        83 --------------------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~  118 (166)
T 3md3_A           83 --------------------------------------------SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH  118 (166)
T ss_dssp             --------------------------------------------CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEE
T ss_pred             --------------------------------------------CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEE
Confidence                                                        111247999999999999999999999999999999


Q ss_pred             EeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEcc
Q 005812          457 PVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKAL  508 (676)
Q Consensus       457 i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~  508 (676)
                      ++.+..++.++|||||+|.+.++|.+|+..||     |..|+|++|.|.||.
T Consensus       119 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ-----GQDLNGRPLRINWAA  165 (166)
T ss_dssp             EEECTTTCCEEEEEEEEESCHHHHHHHHHHHT-----TCEETTEECEEEESC
T ss_pred             EEecCCCCCcceEEEEEeCCHHHHHHHHHHhC-----CCccCCcEEEEEecC
Confidence            99998899999999999999999999999999     999999999999985

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

Probab=99.97  E-value=1.2e-29  Score=238.02  Aligned_cols=164  Identities=20%  Similarity=0.359  Sum_probs=151.0

Q ss_pred             cEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCeE
Q 005812          122 RTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGGT  201 (676)
Q Consensus       122 ~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~  201 (676)
                      |+|||+|||+++++++|+++|+.||.|.++.++.++          .|+++|||||+|.+.++|.+|+..|||..+.|+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~----------~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~   70 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK----------NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNI   70 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC----------C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC----------CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCe
Confidence            589999999999999999999999999999998764          3788999999999999999999999999999999


Q ss_pred             EEEecCCC--CCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhC
Q 005812          202 VWARQLGG--EGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN  279 (676)
Q Consensus       202 i~v~~~~~--~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  279 (676)
                      +.+.....  .......++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..||
T Consensus        71 i~v~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  150 (166)
T 3md3_A           71 VKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ  150 (166)
T ss_dssp             CEEEECCCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHT
T ss_pred             eEEEEcCCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Confidence            99875433  2345567899999999999999999999999999999999998899999999999999999999999999


Q ss_pred             CceeCCeeEEEEEecC
Q 005812          280 GQKFGKRPIAVDWAVP  295 (676)
Q Consensus       280 ~~~~~g~~i~v~~a~~  295 (676)
                      |..+.|+.|.|.|+.+
T Consensus       151 g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          151 GQDLNGRPLRINWAAK  166 (166)
T ss_dssp             TCEETTEECEEEESCC
T ss_pred             CCccCCcEEEEEecCC
Confidence            9999999999999853

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-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

Probab=99.97  E-value=1.3e-29  Score=238.26  Aligned_cols=164  Identities=18%  Similarity=0.265  Sum_probs=154.0

Q ss_pred             CcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCe
Q 005812          121 ARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGG  200 (676)
Q Consensus       121 ~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~  200 (676)
                      .++|||+|||+++++++|+++|+.||.|.++.++.++.         .|+++|||||+|.+.++|.+|+..|++..+.|+
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~---------~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~   73 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYK---------TGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNK   73 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETT---------TTEECSEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCC---------CCccceEEEEEECCHHHHHHHHHhcCCCEeCCc
Confidence            57899999999999999999999999999999886653         488999999999999999999999999999999


Q ss_pred             EEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCC
Q 005812          201 TVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG  280 (676)
Q Consensus       201 ~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~  280 (676)
                      .|.+............++|||+|||..+++++|+++|++||.|..+.++++..+|.++|||||+|.+.++|.+|++.|||
T Consensus        74 ~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g  153 (168)
T 1b7f_A           74 RLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN  153 (168)
T ss_dssp             ECEEEECCCCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             EEEEEecCCCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcC
Confidence            99998777666677889999999999999999999999999999999999988899999999999999999999999999


Q ss_pred             ceeCC--eeEEEEEe
Q 005812          281 QKFGK--RPIAVDWA  293 (676)
Q Consensus       281 ~~~~g--~~i~v~~a  293 (676)
                      ..+.|  ++|+|.||
T Consensus       154 ~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          154 VIPEGGSQPLSVRLA  168 (168)
T ss_dssp             CCCTTCSSCCEEEEC
T ss_pred             CEecCCCeEEEEEeC
Confidence            99977  99999986

>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

Probab=99.97  E-value=1.1e-30  Score=245.35  Aligned_cols=165  Identities=21%  Similarity=0.423  Sum_probs=151.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      +.++|||+|||+++++++|+++|+.||.|.+|.+++++.+|.++|||||+|.+.++|.+|+..  +..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            457999999999999999999999999999999999988999999999999999999999994  678999999999875


Q ss_pred             CCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCC
Q 005812          295 PKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSL  374 (676)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  374 (676)
                      +...                                                                            
T Consensus        80 ~~~~----------------------------------------------------------------------------   83 (167)
T 2cjk_A           80 PRDE----------------------------------------------------------------------------   83 (167)
T ss_dssp             CHHH----------------------------------------------------------------------------
T ss_pred             chhh----------------------------------------------------------------------------
Confidence            4310                                                                            


Q ss_pred             CCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE
Q 005812          375 SDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS  454 (676)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~  454 (676)
                                                                     ..+.++|||+|||+.+++++|+++|++||.|..
T Consensus        84 -----------------------------------------------~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~  116 (167)
T 2cjk_A           84 -----------------------------------------------QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIID  116 (167)
T ss_dssp             -----------------------------------------------HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSE
T ss_pred             -----------------------------------------------ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEE
Confidence                                                           001368999999999999999999999999999


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCc
Q 005812          455 FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK  510 (676)
Q Consensus       455 v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k  510 (676)
                      +.++.+..++.++|||||+|.+.++|.+|++ ++     +..|+|++|.|.+|.++
T Consensus       117 ~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~-----~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          117 AQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NK-----FIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             EECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CS-----EECSSSSCEEEEECCCC
T ss_pred             EEEEEcCCCCccceEEEEEECCHHHHHHHHh-CC-----CEEeCCeEEEEeecCCC
Confidence            9999998889999999999999999999997 88     99999999999999886

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

Probab=99.97  E-value=8.1e-30  Score=249.38  Aligned_cols=167  Identities=19%  Similarity=0.219  Sum_probs=150.2

Q ss_pred             cCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecC
Q 005812          120 VARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKG  199 (676)
Q Consensus       120 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~  199 (676)
                      ..++|||+|||+++++++|+++|++||+|.+|+|+.++.         .|+++|||||+|.+.++|.+|+..+|+..+.|
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~---------tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g   84 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMI---------TRRSLGYAYVNFQQPADAERALDTMNFDVIKG   84 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT---------TCCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccC---------CCCccccccceeCCHHHHHHHHHHhhhhhcCC
Confidence            457999999999999999999999999999999998764         48899999999999999999999999999999


Q ss_pred             eEEEEecCCCCC--CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHH
Q 005812          200 GTVWARQLGGEG--SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK  277 (676)
Q Consensus       200 ~~i~v~~~~~~~--~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~  277 (676)
                      +.+.+.......  ......+|||+|||+.+++++|+++|+.||.|..|.|+++.  +.++|||||+|.+.++|.+|++.
T Consensus        85 ~~i~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~  162 (213)
T 4f02_A           85 KPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK  162 (213)
T ss_dssp             EECEEEECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHH
T ss_pred             cccccccccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHH
Confidence            999886543222  12345789999999999999999999999999999999874  45899999999999999999999


Q ss_pred             hCCceeCCeeEEEEEecCCC
Q 005812          278 FNGQKFGKRPIAVDWAVPKN  297 (676)
Q Consensus       278 l~~~~~~g~~i~v~~a~~~~  297 (676)
                      |||..|.|+.|.|.|+.++.
T Consensus       163 lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          163 MNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             HTTCEETTEECEEEECCCHH
T ss_pred             hCCCEECCEEEEEEEcCCCc
Confidence            99999999999999998754

>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

Probab=99.97  E-value=2.2e-29  Score=236.35  Aligned_cols=164  Identities=26%  Similarity=0.335  Sum_probs=152.7

Q ss_pred             CcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCe
Q 005812          121 ARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGG  200 (676)
Q Consensus       121 ~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~  200 (676)
                      .++|||+|||+++++++|+++|+.||.|.++.++.++.         .|+++|||||+|.+.++|.+|+..|++..+.|+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~---------~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~   72 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI---------TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK   72 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTT---------TCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC---------CCcceeEEEEEECCHHHHHHHHHHcCCCccCCc
Confidence            46899999999999999999999999999999987653         488999999999999999999999999999999


Q ss_pred             EEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCC
Q 005812          201 TVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG  280 (676)
Q Consensus       201 ~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~  280 (676)
                      .|.+............++|||+|||..+++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|.+|++.|||
T Consensus        73 ~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g  152 (167)
T 1fxl_A           73 TIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG  152 (167)
T ss_dssp             ECEEEECCCCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             eEEEEecCCCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcC
Confidence            99998776666666788999999999999999999999999999999999988999999999999999999999999999


Q ss_pred             ceeCCee--EEEEEe
Q 005812          281 QKFGKRP--IAVDWA  293 (676)
Q Consensus       281 ~~~~g~~--i~v~~a  293 (676)
                      ..+.|+.  |.|.||
T Consensus       153 ~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          153 QKPSGATEPITVKFA  167 (167)
T ss_dssp             CCCTTCSSCCEEEEC
T ss_pred             CccCCCccceEEEeC
Confidence            9999965  888875

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

Probab=99.97  E-value=4.8e-30  Score=251.80  Aligned_cols=180  Identities=25%  Similarity=0.390  Sum_probs=154.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++|||+|||.++++++|+++|+.||.|.+|.+++++.++.++|||||+|.+.++|.+|++.|++..|.|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            35799999999999999999999999999999999998899999999999999999999999999999999999998875


Q ss_pred             CCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCC
Q 005812          295 PKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSL  374 (676)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  374 (676)
                      .....                                                      .........            
T Consensus       107 ~~~~~------------------------------------------------------~~~~~~~~~------------  120 (216)
T 2qfj_A          107 NIGQA------------------------------------------------------QPIIDQLAE------------  120 (216)
T ss_dssp             CCGGG------------------------------------------------------HHHHHHHHH------------
T ss_pred             Ccccc------------------------------------------------------chhhhhhhc------------
Confidence            43210                                                      000000000            


Q ss_pred             CCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE
Q 005812          375 SDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS  454 (676)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~  454 (676)
                                                                    .....++|||+|||+.+++++|+++|+.||.|..
T Consensus       121 ----------------------------------------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~  154 (216)
T 2qfj_A          121 ----------------------------------------------EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKS  154 (216)
T ss_dssp             ----------------------------------------------HHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEE
T ss_pred             ----------------------------------------------ccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeE
Confidence                                                          1112479999999999999999999999999999


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCch
Q 005812          455 FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       455 v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~  511 (676)
                      |+++.+..++.++|||||+|.+.++|.+|+..||     |..|+|+.|.|.++.++.
T Consensus       155 v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~-----g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          155 ATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN-----LFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-----TCBCSSSBCEEEECSSCS
T ss_pred             EEEEecCCCCCcCceEEEEecCHHHHHHHHHHcc-----CCEeCCcEEEEEEecCCC
Confidence            9999998899999999999999999999999999     999999999999998764

>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

Probab=99.96  E-value=6.9e-30  Score=239.95  Aligned_cols=165  Identities=20%  Similarity=0.286  Sum_probs=149.5

Q ss_pred             cCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecC
Q 005812          120 VARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKG  199 (676)
Q Consensus       120 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~  199 (676)
                      ..++|||+|||+++++++|+++|+.||.|.++.++.++.         .|+++|||||+|.+.++|.+|+..  +..+.|
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~---------~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g   70 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPA---------TGRSRGFGFLSFEKPSSVDEVVKT--QHILDG   70 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTT---------TSSCCSCEEEEESSTHHHHHHHHS--CCEETT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCC---------CCCccceEEEEEccHHHHHHHHhc--ccccCC
Confidence            357999999999999999999999999999999987763         489999999999999999999984  678899


Q ss_pred             eEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhC
Q 005812          200 GTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN  279 (676)
Q Consensus       200 ~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  279 (676)
                      +.+.+............++|||+|||..+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+|++ ++
T Consensus        71 ~~i~v~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~  149 (167)
T 2cjk_A           71 KVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NK  149 (167)
T ss_dssp             EECCCEECCCHHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CS
T ss_pred             eEcccccccchhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CC
Confidence            98887654433334456799999999999999999999999999999999998899999999999999999999998 89


Q ss_pred             CceeCCeeEEEEEecCC
Q 005812          280 GQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       280 ~~~~~g~~i~v~~a~~~  296 (676)
                      +..+.|+.|.|.|+.|+
T Consensus       150 ~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          150 FIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             EECSSSSCEEEEECCCC
T ss_pred             CEEeCCeEEEEeecCCC
Confidence            99999999999999876

>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

Probab=99.96  E-value=5.5e-29  Score=235.63  Aligned_cols=165  Identities=19%  Similarity=0.311  Sum_probs=146.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCC--CceeEEEEEecCHHHHHHHHHHhCCceeC---CeeEE
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTG--LSKGFAFVKFTCKRDAESAIQKFNGQKFG---KRPIA  289 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~A~~~l~~~~~~---g~~i~  289 (676)
                      ..++|||+|||+++++++|+++|++||.|.+|.+++++.++  .++|||||+|.+.++|.+|++.|++..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            46799999999999999999999999999999999998776  89999999999999999999999998875   67788


Q ss_pred             EEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCC
Q 005812          290 VDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTG  369 (676)
Q Consensus       290 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g  369 (676)
                      +.++.+...                                                                       
T Consensus        82 ~~~~~~~~~-----------------------------------------------------------------------   90 (175)
T 3nmr_A           82 MKPADSEKN-----------------------------------------------------------------------   90 (175)
T ss_dssp             EEECGGGCC-----------------------------------------------------------------------
T ss_pred             Ecccccccc-----------------------------------------------------------------------
Confidence            877644321                                                                       


Q ss_pred             CCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhC
Q 005812          370 SLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAF  449 (676)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~  449 (676)
                                                                         .....++|||+|||+.+++++|+++|++|
T Consensus        91 ---------------------------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~  119 (175)
T 3nmr_A           91 ---------------------------------------------------NAVEDRKLFIGMISKKCTENDIRVMFSSF  119 (175)
T ss_dssp             ---------------------------------------------------SCGGGSEEEEESCCTTCCHHHHHHHHGGG
T ss_pred             ---------------------------------------------------ccCCCCeEEEcCCCCcCCHHHHHHHHHhC
Confidence                                                               01124799999999999999999999999


Q ss_pred             CceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec---CcEEEEEEc
Q 005812          450 GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK---GRQLTVLKA  507 (676)
Q Consensus       450 G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~---gr~l~v~~a  507 (676)
                      |.|..+.++.+. +|.++|||||+|.+.++|.+|+..||     |..+.   |++|.|.||
T Consensus       120 G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          120 GQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMH-----QAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             SCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHT-----TSCCCTTCSSCCEEEEC
T ss_pred             CCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhc-----CCcccCCCCCCeEEEec
Confidence            999999999885 58899999999999999999999999     87776   499999997

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

Probab=99.96  E-value=8.2e-29  Score=243.01  Aligned_cols=171  Identities=14%  Similarity=0.237  Sum_probs=153.1

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeec
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIK  198 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~  198 (676)
                      ...++|||+|||.++++++|+++|+.||.|.+|.++.++.         .|+++|||||+|.+.++|.+|+..||+..+.
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~---------~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~   96 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSV---------TMKHKGFAFVEYEVPEAAQLALEQMNSVMLG   96 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-C---------C-CCCSEEEEEESSHHHHHHHHHHHSSCCCC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCC---------CCccCceEEEEeCCHHHHHHHHHHccCCeeC
Confidence            4567999999999999999999999999999999987753         4889999999999999999999999999999


Q ss_pred             CeEEEEecCCCCC-----------CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecC
Q 005812          199 GGTVWARQLGGEG-----------SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC  267 (676)
Q Consensus       199 ~~~i~v~~~~~~~-----------~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~  267 (676)
                      |+.|.|.......           .....++|||+|||..+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+
T Consensus        97 g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~  176 (216)
T 2qfj_A           97 GRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEK  176 (216)
T ss_dssp             -CCCEEECCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CeeEEEecCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecC
Confidence            9999996543222           12345899999999999999999999999999999999998899999999999999


Q ss_pred             HHHHHHHHHHhCCceeCCeeEEEEEecCCCC
Q 005812          268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNI  298 (676)
Q Consensus       268 ~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~  298 (676)
                      .++|.+|++.|||..|.|+.|.|.|+.++..
T Consensus       177 ~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~  207 (216)
T 2qfj_A          177 AQSSQDAVSSMNLFDLGGQYLRVGKAVTPPM  207 (216)
T ss_dssp             HHHHHHHHHHHTTCBCSSSBCEEEECSSCSS
T ss_pred             HHHHHHHHHHccCCEeCCcEEEEEEecCCCC
Confidence            9999999999999999999999999987643

>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

Probab=99.96  E-value=1e-28  Score=238.51  Aligned_cols=170  Identities=18%  Similarity=0.232  Sum_probs=148.7

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeec
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIK  198 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~  198 (676)
                      ...++|||+|||+++++++|+++|+.||.|.+|.++.++.         .|+++|||||+|.+.++|.+|+.. ++..+.
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~---------~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~   80 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN---------TKRSRGFGFVTYATVEEVDAAMNA-RPHKVD   80 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT---------TCCEEEEEEEEESSHHHHHHHHHT-CSCEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCC---------CCCccceEEEEeCCHHHHHHHHhc-CCCEEC
Confidence            4578999999999999999999999999999999987763         488999999999999999999985 999999


Q ss_pred             CeEEEEecCCCCC------CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHH
Q 005812          199 GGTVWARQLGGEG------SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAE  272 (676)
Q Consensus       199 ~~~i~v~~~~~~~------~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~  272 (676)
                      |+.|.+.......      .....++|||+|||+.+++++|+++|+.||.|..|.++.+..+|.++|||||+|.+.++|.
T Consensus        81 g~~l~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~  160 (196)
T 1l3k_A           81 GRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD  160 (196)
T ss_dssp             TEECEEEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CEEeeeecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHH
Confidence            9999987543221      2234589999999999999999999999999999999999889999999999999999999


Q ss_pred             HHHHHhCCceeCCeeEEEEEecCCCCC
Q 005812          273 SAIQKFNGQKFGKRPIAVDWAVPKNIY  299 (676)
Q Consensus       273 ~A~~~l~~~~~~g~~i~v~~a~~~~~~  299 (676)
                      +|+.. ++..|.|+.|.|.|+.++...
T Consensus       161 ~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          161 KIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             HHHHC-SCCEETTEECEEEECC-----
T ss_pred             HHHHh-CCcEECCEEEEEEecCChhHh
Confidence            99996 899999999999999887643

>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

Probab=99.96  E-value=2.3e-28  Score=230.78  Aligned_cols=158  Identities=26%  Similarity=0.442  Sum_probs=143.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccC----C-------ceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPV----G-------LVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF  283 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~----G-------~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  283 (676)
                      +.++|||+|||+++++++|+++|+.|    |       .|.++.+.+      ++|||||+|.+.++|.+|+ .|+|..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            46799999999999999999999999    6       777777765      5799999999999999999 7999999


Q ss_pred             CCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhc
Q 005812          284 GKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNK  363 (676)
Q Consensus       284 ~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  363 (676)
                      .|+.|.|.++.+...                                                                 
T Consensus        76 ~g~~i~v~~~~~~~~-----------------------------------------------------------------   90 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQP-----------------------------------------------------------------   90 (172)
T ss_dssp             TTEECEEECCSSCCC-----------------------------------------------------------------
T ss_pred             cCceeeecCCcccCC-----------------------------------------------------------------
Confidence            999999998643210                                                                 


Q ss_pred             ccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHH
Q 005812          364 LTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVK  443 (676)
Q Consensus       364 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~  443 (676)
                                                                                ....++|||+|||..+++++|+
T Consensus        91 ----------------------------------------------------------~~~~~~l~v~nlp~~~t~~~l~  112 (172)
T 2g4b_A           91 ----------------------------------------------------------LPGAHKLFIGGLPNYLNDDQVK  112 (172)
T ss_dssp             ----------------------------------------------------------CTTTTCEEEECCCTTCCHHHHH
T ss_pred             ----------------------------------------------------------CCCCCEEEEEcCCCcCCHHHHH
Confidence                                                                      0113689999999999999999


Q ss_pred             HHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEc
Q 005812          444 QRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA  507 (676)
Q Consensus       444 ~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a  507 (676)
                      ++|++||.|..+.++.+..+|.++|||||+|.+.++|.+|+..||     |..|+|++|.|.||
T Consensus       113 ~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          113 ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN-----GMQLGDKKLLVQRA  171 (172)
T ss_dssp             HHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHT-----TCEETTEECEEEEC
T ss_pred             HHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcC-----CCEECCeEEEEEeC
Confidence            999999999999999998899999999999999999999999999     99999999999997

>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

Probab=99.96  E-value=3.5e-28  Score=229.43  Aligned_cols=159  Identities=19%  Similarity=0.310  Sum_probs=147.1

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcC----C-------CeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHH
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSI----G-------TVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACA  187 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~----G-------~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~  187 (676)
                      +..++|||+|||+++++++|+++|+.|    |       .|.++.+               ++++|||||+|.+.++|.+
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~---------------~~~~g~afV~f~~~~~A~~   66 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI---------------NQDKNFAFLEFRSVDETTQ   66 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE---------------ETTTTEEEEEESSHHHHHH
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEe---------------cCCCCEEEEEeCCHHHHHH
Confidence            346899999999999999999999999    6       6777764               3568999999999999999


Q ss_pred             HHHHhCCCeecCeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecC
Q 005812          188 SVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC  267 (676)
Q Consensus       188 A~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~  267 (676)
                      |+ .+|+..+.|+.+.+............++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+
T Consensus        67 A~-~~~~~~~~g~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~  145 (172)
T 2g4b_A           67 AM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD  145 (172)
T ss_dssp             HG-GGTTCEETTEECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESS
T ss_pred             HH-HhCCcEecCceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCC
Confidence            99 89999999999999877666666678999999999999999999999999999999999998899999999999999


Q ss_pred             HHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          268 KRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       268 ~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      .++|.+|++.|||..++|+.|.|.||
T Consensus       146 ~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          146 INVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             HHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            99999999999999999999999997

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

Probab=99.96  E-value=7.9e-28  Score=232.60  Aligned_cols=182  Identities=24%  Similarity=0.371  Sum_probs=147.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccC----C-------ceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPV----G-------LVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF  283 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~----G-------~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  283 (676)
                      ..++|||+|||+++++++|+++|+.|    |       .|.++.+..      ++|||||+|.+.++|.+|+ .|+|..|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~------~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEET------TTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecC------CCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            45799999999999999999999999    5       566666643      6799999999999999999 7999999


Q ss_pred             CCeeEEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhc
Q 005812          284 GKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNK  363 (676)
Q Consensus       284 ~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  363 (676)
                      .|+.|.|.++.+..........         ...                                              
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~~---------~~~----------------------------------------------  100 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQPLPGMSEN---------PSV----------------------------------------------  100 (198)
T ss_dssp             TTEEEEEECCCCCCCCCCSSSC---------SSC----------------------------------------------
T ss_pred             cCceEEEeCCCCCCCCCCCcCC---------CcC----------------------------------------------
Confidence            9999999988654321100000         000                                              


Q ss_pred             ccccCCCCCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHH
Q 005812          364 LTSTTGSLPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVK  443 (676)
Q Consensus       364 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~  443 (676)
                            ..+                                          .........+.++|||+|||+.+++++|+
T Consensus       101 ------~~~------------------------------------------~~~~~~~~~~~~~l~v~nl~~~~~~~~l~  132 (198)
T 2yh0_A          101 ------YVP------------------------------------------GVVSTVVPDSAHKLFIGGLPNYLNDDQVK  132 (198)
T ss_dssp             ------CCT------------------------------------------TSSCCCSSCCCCEEEEECCCTTCCHHHHH
T ss_pred             ------CCC------------------------------------------CCccCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence                  000                                          00000012345899999999999999999


Q ss_pred             HHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCch
Q 005812          444 QRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       444 ~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~  511 (676)
                      ++|++||.|..+.++.+..++.++|||||+|.+.++|.+|+..||     |..|+|+.|.|.++.++.
T Consensus       133 ~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          133 ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN-----GMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             HHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHT-----TCEETTEECEEEESCCCC
T ss_pred             HHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcC-----CCEECCEEEEEEECCCCC
Confidence            999999999999999998889999999999999999999999999     999999999999998764

>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

Probab=99.96  E-value=9.4e-28  Score=232.16  Aligned_cols=195  Identities=14%  Similarity=0.149  Sum_probs=144.1

Q ss_pred             CCcEEEEcCCC-CCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          215 QKWKLIIRNIP-FKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       215 ~~~~v~V~nLp-~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      +.++|||+||| ..+++++|+++|+.||.|.+|+|+++     ++|||||+|.+.++|+.|++.|||..+.|+.|+|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            56799999999 89999999999999999999999875     4799999999999999999999999999999999998


Q ss_pred             cCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCC
Q 005812          294 VPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPS  373 (676)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  373 (676)
                      ............          ..      +........          .......+.....                  
T Consensus        78 ~~~~~~p~~~~~----------~~------~~~~~~~~~----------~~~~~~r~~~~~~------------------  113 (205)
T 3tyt_A           78 KQPAIMPGQSYG----------LE------DGSCSYKDF----------SESRNNRFSTPEQ------------------  113 (205)
T ss_dssp             SCSCCCCCSCCB----------CT------TSCBSEEEC----------TTCTTCSCSSHHH------------------
T ss_pred             cCCccCCCcccc----------cc------cCCcccccc----------CCCccccccCccc------------------
Confidence            654321000000          00      000000000          0000000000000                  


Q ss_pred             CCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCce-
Q 005812          374 LSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEV-  452 (676)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v-  452 (676)
                                                                ........++++|||+|||+.+++++|+++|++||.| 
T Consensus       114 ------------------------------------------~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~  151 (205)
T 3tyt_A          114 ------------------------------------------AAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKR  151 (205)
T ss_dssp             ------------------------------------------HTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCC
T ss_pred             ------------------------------------------ccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcc
Confidence                                                      0000012346799999999999999999999999999 


Q ss_pred             -eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc----EEEEEEc
Q 005812          453 -VSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR----QLTVLKA  507 (676)
Q Consensus       453 -~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr----~l~v~~a  507 (676)
                       .+++++.+.  +.++|+|||+|.+.++|.+|+..||     |..|.|+    ++.|.+|
T Consensus       152 ~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~ln-----g~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          152 PTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLN-----HYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHT-----TCEECCSSSSSCEECEEE
T ss_pred             eEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhC-----CCCccCCCCCcceEEEec
Confidence             899888764  4567999999999999999999999     9999987    6777775

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.96  E-value=1.1e-28  Score=233.74  Aligned_cols=166  Identities=22%  Similarity=0.334  Sum_probs=145.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||.++++++|+++|..||.+.. .++.+..++.++|||||+|.+.++|.+|++ |+|..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            4567899999999999999999999999998776 344455678899999999999999999995 99999999999999


Q ss_pred             EecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCC
Q 005812          292 WAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSL  371 (676)
Q Consensus       292 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  371 (676)
                      ++.++...                                                                        
T Consensus        87 ~~~~~~~~------------------------------------------------------------------------   94 (175)
T 1fje_B           87 KPKGRDSK------------------------------------------------------------------------   94 (175)
T ss_dssp             CCCCSSCS------------------------------------------------------------------------
T ss_pred             cCCCcccc------------------------------------------------------------------------
Confidence            98654210                                                                        


Q ss_pred             CCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCc
Q 005812          372 PSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGE  451 (676)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~  451 (676)
                                                                       .....++|||+|||+.+++++|+++|+.||.
T Consensus        95 -------------------------------------------------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~  125 (175)
T 1fje_B           95 -------------------------------------------------KVRAARTLLAKNLSFNITEDELKEVFEDALE  125 (175)
T ss_dssp             -------------------------------------------------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSE
T ss_pred             -------------------------------------------------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCe
Confidence                                                             0112479999999999999999999999998


Q ss_pred             eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCc
Q 005812          452 VVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK  510 (676)
Q Consensus       452 v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k  510 (676)
                      |..+     ..++.++|||||+|.+.++|.+|+..||     |..|+|+.|.|.||.+|
T Consensus       126 v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          126 IRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQ-----GAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             EEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHT-----EEEETTEEEEEEECSSC
T ss_pred             EEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhC-----CCEECCeEEEEEecCCC
Confidence            8765     4578899999999999999999999999     99999999999999876

>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

Probab=99.95  E-value=1.1e-27  Score=226.61  Aligned_cols=167  Identities=21%  Similarity=0.271  Sum_probs=145.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCC--CcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec---C
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTK--RPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK---G  499 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~--~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~---g  499 (676)
                      .++|||+|||+++++++|+++|++||.|.+|+++++..++  .++|||||+|.+.++|.+|+..|+     +..+.   +
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-----~~~~~~~~~   77 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALH-----NMKVLPGMH   77 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHT-----TTCCCTTCS
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhc-----CcEEccCCc
Confidence            4799999999999999999999999999999999998776  899999999999999999999999     77765   6


Q ss_pred             cEEEEEEccCchhhhhHhhhhhcccccccCcccccccCcccCCCCCCCCCChhHHHHHHHHHHHHhhcCCCCCccccCCe
Q 005812          500 RQLTVLKALDKKLAHDKEIDKSKNETNDHRNLYLAKEGLILEGTPAAEGVSDDDMSKRQMLHEKKMTKLQSPNFHVSRTR  579 (676)
Q Consensus       500 r~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~  579 (676)
                      +.+.+.++.+....                                                            ....++
T Consensus        78 ~~~~~~~~~~~~~~------------------------------------------------------------~~~~~~   97 (175)
T 3nmr_A           78 HPIQMKPADSEKNN------------------------------------------------------------AVEDRK   97 (175)
T ss_dssp             SCCEEEECGGGCCS------------------------------------------------------------CGGGSE
T ss_pred             cceEEccccccccc------------------------------------------------------------cCCCCe
Confidence            78888876543210                                                            013368


Q ss_pred             EEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCCC
Q 005812          580 LVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNPS  659 (676)
Q Consensus       580 l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~~  659 (676)
                      |||+|||..+|+++|+++|+         .||.|.+|+++++..       +.++|+|||+|.++++|.+|++.|||..+
T Consensus        98 l~v~nl~~~~t~~~l~~~F~---------~~G~i~~v~~~~~~~-------g~~~g~afV~f~~~~~A~~A~~~l~g~~~  161 (175)
T 3nmr_A           98 LFIGMISKKCTENDIRVMFS---------SFGQIEECRILRGPD-------GLSRGCAFVTFTTRAMAQTAIKAMHQAQT  161 (175)
T ss_dssp             EEEESCCTTCCHHHHHHHHG---------GGSCEEEEEEEECTT-------SCEEEEEEEEESSHHHHHHHHHHHTTSCC
T ss_pred             EEEcCCCCcCCHHHHHHHHH---------hCCCEEEEEEEECCC-------CCEEEEEEEEECCHHHHHHHHHHhcCCcc
Confidence            99999999999999999999         699999999998842       47899999999999999999999999876


Q ss_pred             CCCcccCcccccc
Q 005812          660 KLFYHHCFDAADA  672 (676)
Q Consensus       660 ~~~~~~~~~~~~~  672 (676)
                      ..|..+.+.|.+|
T Consensus       162 ~~g~~~~l~V~~a  174 (175)
T 3nmr_A          162 MEGCSSPMVVKFA  174 (175)
T ss_dssp             CTTCSSCCEEEEC
T ss_pred             cCCCCCCeEEEec
Confidence            6555688888877

>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

Probab=99.95  E-value=2.2e-26  Score=235.44  Aligned_cols=254  Identities=18%  Similarity=0.250  Sum_probs=153.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH----HhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCee
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIK----DMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRP  287 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~----~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  287 (676)
                      .....++|||+|||+++++++|+    ++|+.||.|.+|++++   +++++|||||+|.+.++|.+|++.|||..|.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            34567899999999999999976    8999999999999986   6779999999999999999999999999999999


Q ss_pred             EEEEEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhc--cc
Q 005812          288 IAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNK--LT  365 (676)
Q Consensus       288 i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~  365 (676)
                      |.|.|+........................+....                              ...........  ..
T Consensus        82 l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------------------~~~~~~~~~~~~~~~  131 (282)
T 3pgw_A           82 MRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQ------------------------------ETPATKKAVQGGGAT  131 (282)
T ss_pred             EEEEEeccCcchhhhhcCCcccchhhhhhhhcccc------------------------------chhhhhhhccCcCCc
Confidence            99999966543211111000000000000000000                              00000000000  00


Q ss_pred             ----ccCCCCCCCCCccccc------cCCCCCCCchh-hcccccccc-ccccCCC--CCCCC--CCCcccCCCCCCCeEE
Q 005812          366 ----STTGSLPSLSDDSALV------KGNKEQDSDKT-VNESAKVSD-VSKLNSS--KSKPK--SLKQTEGEDELQNTIF  429 (676)
Q Consensus       366 ----~~~g~~~~~~~~~~~~------~~~~~~~~~~~-~~~~~~~~~-~~~~~~~--~~~~~--~~~~~~~~~~~~~~l~  429 (676)
                          ...+..++........      .|......... ......... ..+....  ...+.  ..........++++||
T Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  211 (282)
T 3pgw_A          132 PVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILF  211 (282)
T ss_pred             ccCCCCCCCCCCCCcccccccccccCCCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEE
Confidence                0000000000000000      00000000000 000000000 0000000  00000  0001113445678999


Q ss_pred             EcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec-CcEEEEEEcc
Q 005812          430 ICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK-GRQLTVLKAL  508 (676)
Q Consensus       430 V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~-gr~l~v~~a~  508 (676)
                      |+|||..+++++|+++|++||.|.+|+++.+.     +|||||+|.+.++|.+|+..||     |..|+ |+.|.|.|++
T Consensus       212 v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~-----g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          212 LTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQ-----GFKITQNNAMKISFAK  281 (282)
T ss_pred             EeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcC-----CcEeCCCCEEEEEEec
Confidence            99999999999999999999999999988552     6899999999999999999999     99999 9999999985

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

Probab=99.95  E-value=4.7e-27  Score=227.12  Aligned_cols=163  Identities=19%  Similarity=0.302  Sum_probs=144.5

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcC----C-------CeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHH
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSI----G-------TVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACA  187 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~----G-------~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~  187 (676)
                      +..++|||+|||+++++++|+++|+.|    |       .|..+.+               ++++|||||+|.+.++|.+
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~---------------~~~~g~afV~F~~~~~A~~   66 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI---------------NQDKNFAFLEFRSVDETTQ   66 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE---------------ETTTTEEEEEESCSHHHHH
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe---------------cCCCCEEEEEeCCHHHHHH
Confidence            346899999999999999999999999    4       5555553               4678999999999999999


Q ss_pred             HHHHhCCCeecCeEEEEecCCCCC--------------------CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEE
Q 005812          188 SVALLHQKEIKGGTVWARQLGGEG--------------------SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVY  247 (676)
Q Consensus       188 A~~~l~~~~~~~~~i~v~~~~~~~--------------------~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~  247 (676)
                      |+ .|||..+.|+.|.+.......                    .....++|||+|||..+++++|+++|++||.|..|.
T Consensus        67 Al-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~  145 (198)
T 2yh0_A           67 AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFN  145 (198)
T ss_dssp             HG-GGTTEEETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEE
T ss_pred             HH-HhcCCEEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEE
Confidence            99 899999999999987543211                    124568999999999999999999999999999999


Q ss_pred             EcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCC
Q 005812          248 IPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKN  297 (676)
Q Consensus       248 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~  297 (676)
                      ++.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+.++.
T Consensus       146 ~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          146 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             EEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             EeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            99998899999999999999999999999999999999999999998764

>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

Probab=99.95  E-value=6.3e-27  Score=231.54  Aligned_cols=196  Identities=19%  Similarity=0.205  Sum_probs=149.3

Q ss_pred             CCCCCcEEEEcCCCC-CCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          212 SKTQKWKLIIRNIPF-KAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~-~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      .....++|||+|||+ ++++++|+++|+.||.|.+|.+++++     +|||||+|.+.++|.+|++.|+|..|.|+.|.|
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v  104 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345678999999999 99999999999999999999999863     789999999999999999999999999999999


Q ss_pred             EEecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCC
Q 005812          291 DWAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGS  370 (676)
Q Consensus       291 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~  370 (676)
                      .|+.+.............        .          .....                                      
T Consensus       105 ~~a~~~~~~~~~~~~~~~--------~----------~~~~~--------------------------------------  128 (229)
T 2adc_A          105 TLSKHQNVQLPREGQEDQ--------G----------LTKDY--------------------------------------  128 (229)
T ss_dssp             ECCSCCCCCCCCSSSSTT--------T----------TEEEC--------------------------------------
T ss_pred             EEecCccccCcccccccc--------c----------ccccc--------------------------------------
Confidence            999765432211000000        0          00000                                      


Q ss_pred             CCCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCC
Q 005812          371 LPSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFG  450 (676)
Q Consensus       371 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G  450 (676)
                                                      ......+...+..........++++|||+|||+.+++++|+++|++||
T Consensus       129 --------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G  176 (229)
T 2adc_A          129 --------------------------------GNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNG  176 (229)
T ss_dssp             --------------------------------TTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTS
T ss_pred             --------------------------------ccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcC
Confidence                                            000000000000000011233468999999999999999999999999


Q ss_pred             -ceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec-CcEEEEEEccCc
Q 005812          451 -EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK-GRQLTVLKALDK  510 (676)
Q Consensus       451 -~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~-gr~l~v~~a~~k  510 (676)
                       .|..|+++.+     .+|||||+|.+.++|.+|+..||     |..++ |+.|.|.|+.++
T Consensus       177 ~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~-----g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          177 GVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLH-----NHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHT-----TCBSSSSCBCEEEECSSC
T ss_pred             CCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHC-----CCccCCCCeEEEEEecCC
Confidence             9999988653     37899999999999999999999     99999 999999998764

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

Probab=99.95  E-value=5.3e-27  Score=226.86  Aligned_cols=193  Identities=20%  Similarity=0.218  Sum_probs=147.2

Q ss_pred             CCcEEEEcCCCC-CCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          215 QKWKLIIRNIPF-KAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       215 ~~~~v~V~nLp~-~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ..++|||+|||+ .+++++|+++|+.||.|.+|.++.++     +|||||+|.+.++|.+|+..|+|..+.|+.|.|.|+
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            457999999999 99999999999999999999999863     789999999999999999999999999999999999


Q ss_pred             cCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCC
Q 005812          294 VPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPS  373 (676)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  373 (676)
                      .+.............                  ......                                    +.   
T Consensus        77 ~~~~~~~~~~~~~~~------------------~~~~~~------------------------------------~~---   99 (198)
T 1qm9_A           77 KHQNVQLPREGQEDQ------------------GLTKDY------------------------------------GN---   99 (198)
T ss_dssp             CCCSCCCSSSSSSSS------------------SCEEES------------------------------------SC---
T ss_pred             cCCCcCCCCcCCccc------------------cccccc------------------------------------cC---
Confidence            765422111000000                  000000                                    00   


Q ss_pred             CCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCC-ce
Q 005812          374 LSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFG-EV  452 (676)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G-~v  452 (676)
                                                     ....+..++..........++++|||+|||..+++++|+++|+.|| .|
T Consensus       100 -------------------------------~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v  148 (198)
T 1qm9_A          100 -------------------------------SPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVV  148 (198)
T ss_dssp             -------------------------------CCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCC
T ss_pred             -------------------------------CchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCc
Confidence                                           0000000000000011223468999999999999999999999999 99


Q ss_pred             eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec-CcEEEEEEccCc
Q 005812          453 VSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK-GRQLTVLKALDK  510 (676)
Q Consensus       453 ~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~-gr~l~v~~a~~k  510 (676)
                      ..++++.+     .+|+|||+|.+.++|.+|+..||     |..++ |++|.|.|+.++
T Consensus       149 ~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~-----g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          149 KGFKFFQK-----DRKMALIQMGSVEEAVQALIDLH-----NHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             CEEEESST-----TSSCEEEECSSHHHHHHHHHHHT-----SSCCSSCCSCCEEEECCC
T ss_pred             eEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhc-----CCccCCCCeEEEEeeccc
Confidence            99988654     27899999999999999999999     99999 999999998764

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.95  E-value=2.1e-27  Score=224.84  Aligned_cols=162  Identities=17%  Similarity=0.270  Sum_probs=141.8

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeec
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIK  198 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~  198 (676)
                      ...++|||+|||.++++++|+++|..||.|..+ ++.+.         ..|+++|||||+|.+.++|.+|+ .||+..+.
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~---------~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~   79 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDV---------RTGTNRKFGYVDFESAEDLEKAL-ELTGLKVF   79 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEE---------EEETTTTEEEEEESSHHHHHHHH-HGGGEEET
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEEC---------CCCccccEEEEEECCHHHHHHHH-hcCCCEeC
Confidence            567899999999999999999999999987662 22222         34889999999999999999999 59999999


Q ss_pred             CeEEEEecCCCC--CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHH
Q 005812          199 GGTVWARQLGGE--GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ  276 (676)
Q Consensus       199 ~~~i~v~~~~~~--~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~  276 (676)
                      |+.|.+......  ......++|||+|||..+++++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|+.
T Consensus        80 g~~l~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~  154 (175)
T 1fje_B           80 GNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLE  154 (175)
T ss_dssp             TEEEEEECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHH
T ss_pred             CeEEEEecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHH
Confidence            999999765432  233456899999999999999999999999988766     3478899999999999999999999


Q ss_pred             HhCCceeCCeeEEEEEecCC
Q 005812          277 KFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       277 ~l~~~~~~g~~i~v~~a~~~  296 (676)
                      .|||..|.|+.|.|.|+.++
T Consensus       155 ~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          155 EKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHTEEEETTEEEEEEECSSC
T ss_pred             HhCCCEECCeEEEEEecCCC
Confidence            99999999999999999875

>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

Probab=99.94  E-value=1.7e-26  Score=233.08  Aligned_cols=160  Identities=28%  Similarity=0.441  Sum_probs=146.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+++|+++|+++|+.||.|..|.+.+      ++|||||+|.+.++|..|+..|+|..+.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~   91 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIR   91 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEee
Confidence            345668999999999999999999999999999999975      46999999999999999999999999999999999


Q ss_pred             EecCCCCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCC
Q 005812          292 WAVPKNIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSL  371 (676)
Q Consensus       292 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  371 (676)
                      |+.+                                                                            
T Consensus        92 ~a~~----------------------------------------------------------------------------   95 (261)
T 3sde_A           92 FATH----------------------------------------------------------------------------   95 (261)
T ss_dssp             ECCC----------------------------------------------------------------------------
T ss_pred             eccc----------------------------------------------------------------------------
Confidence            9743                                                                            


Q ss_pred             CCCCCccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCc
Q 005812          372 PSLSDDSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGE  451 (676)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~  451 (676)
                                                                           +++|||+|||+.+++++|+++|+.||.
T Consensus        96 -----------------------------------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~  122 (261)
T 3sde_A           96 -----------------------------------------------------GAALTVKNLSPVVSNELLEQAFSQFGP  122 (261)
T ss_dssp             -----------------------------------------------------SSEEEEESCCTTCCHHHHHHHHGGGSC
T ss_pred             -----------------------------------------------------CCcccccCCCCCCCHHHHHHHHHhcCC
Confidence                                                                 258999999999999999999999999


Q ss_pred             eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec---CcEEEEEEccCch
Q 005812          452 VVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK---GRQLTVLKALDKK  511 (676)
Q Consensus       452 v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~---gr~l~v~~a~~k~  511 (676)
                      |..|.++.+ .+|.++|||||+|.+.++|.+|+..||.    +..+.   ||+|.|.++.+..
T Consensus       123 i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~----~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          123 VEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGD----GAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             EEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHH----SCEESSSSCCBCEEEECCCEE
T ss_pred             eEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcC----CeEEecCCCceEEEeeccccC
Confidence            999999999 5899999999999999999999999951    55555   9999999998764

>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

Probab=99.94  E-value=2.2e-26  Score=222.53  Aligned_cols=158  Identities=13%  Similarity=0.119  Sum_probs=136.5

Q ss_pred             cCcEEEEcCCC-ccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeec
Q 005812          120 VARTVIIGGLL-NADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIK  198 (676)
Q Consensus       120 ~~~~l~V~nLp-~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~  198 (676)
                      .+++|||+||| ..+++++|+++|+.||.|.+|+++.+              ++|||||+|.+.++|..|+..|||..+.
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~--------------~~g~afV~f~~~~~A~~Ai~~lng~~~~   68 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS--------------KPGAAMVEMADGYAVDRAITHLNNNFMF   68 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT--------------STTCEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC--------------CCCEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            45789999999 89999999999999999999998742              3799999999999999999999999999


Q ss_pred             CeEEEEecCCCCC-------------------------------------CCCCCcEEEEcCCCCCCCHHHHHHhhccCC
Q 005812          199 GGTVWARQLGGEG-------------------------------------SKTQKWKLIIRNIPFKAKVNEIKDMFSPVG  241 (676)
Q Consensus       199 ~~~i~v~~~~~~~-------------------------------------~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G  241 (676)
                      |+.|.|.......                                     ...+.++|||+|||+.+++++|+++|++||
T Consensus        69 g~~l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G  148 (205)
T 3tyt_A           69 GQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELG  148 (205)
T ss_dssp             TEECEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHT
T ss_pred             CceEEEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcC
Confidence            9999986432100                                     012346899999999999999999999999


Q ss_pred             ce--EEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCe----eEEEEEe
Q 005812          242 LV--WNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKR----PIAVDWA  293 (676)
Q Consensus       242 ~i--~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~----~i~v~~a  293 (676)
                      .|  .+++++.+.  +.++|||||+|.+.++|.+|+..|||..|.|.    ++.|.++
T Consensus       149 ~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          149 VKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            99  899998874  45679999999999999999999999999775    5777664

>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

Probab=99.94  E-value=1.2e-25  Score=222.42  Aligned_cols=159  Identities=16%  Similarity=0.222  Sum_probs=140.9

Q ss_pred             ccCcEEEEcCCCc-cccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCee
Q 005812          119 RVARTVIIGGLLN-ADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEI  197 (676)
Q Consensus       119 ~~~~~l~V~nLp~-~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~  197 (676)
                      ..+++|||+|||+ ++++++|+++|+.||.|.+|+++.++              +|||||+|.+.++|.+|+..||+..+
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~--------------~g~afV~F~~~~~A~~Ai~~l~g~~~   97 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--------------KENALVQMADGNQAQLAMSHLNGHKL   97 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT--------------SCCEEEEESCHHHHHHHHHHHTTCBC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC--------------CCEEEEEECCHHHHHHHHHHhCCCeE
Confidence            4578999999999 99999999999999999999987432              78999999999999999999999999


Q ss_pred             cCeEEEEecCCCC-----------------------------------CCCCCCcEEEEcCCCCCCCHHHHHHhhccCC-
Q 005812          198 KGGTVWARQLGGE-----------------------------------GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVG-  241 (676)
Q Consensus       198 ~~~~i~v~~~~~~-----------------------------------~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G-  241 (676)
                      .|+.|.|......                                   ....+.++|||+|||..+++++|+++|+.|| 
T Consensus        98 ~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~  177 (229)
T 2adc_A           98 HGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG  177 (229)
T ss_dssp             SSSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSC
T ss_pred             CCeEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCC
Confidence            9999998643211                                   0012368999999999999999999999999 


Q ss_pred             ceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC-CeeEEEEEecCC
Q 005812          242 LVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG-KRPIAVDWAVPK  296 (676)
Q Consensus       242 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~-g~~i~v~~a~~~  296 (676)
                      .|..|.+..+     .+|||||+|.+.++|.+|+..|+|..+. |+.|.|.|+.++
T Consensus       178 ~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          178 VVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            9999999653     4689999999999999999999999999 999999999764

>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

Probab=99.94  E-value=1.6e-25  Score=229.08  Aligned_cols=159  Identities=15%  Similarity=0.201  Sum_probs=140.9

Q ss_pred             ccCcEEEEcCCCccccHHHHH----HHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCC
Q 005812          119 RVARTVIIGGLLNADMAEEVH----RLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQ  194 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~----~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~  194 (676)
                      ...++|||+|||.++++++|+    ++|+.||.|.+|+++            ++|+++|||||+|.+.++|.+|+..|||
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~------------~~~~~~g~afV~f~~~~~a~~A~~~l~g   74 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS------------RSLKMRGQAFVIFKEVSSATNALRSMQG   74 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEc------------CCCCcceEEEEEECCHHHHHHHHHHhcC
Confidence            457899999999999999966    899999999999966            4588999999999999999999999999


Q ss_pred             CeecCeEEEEecCCCC----------------------------------------------------------------
Q 005812          195 KEIKGGTVWARQLGGE----------------------------------------------------------------  210 (676)
Q Consensus       195 ~~~~~~~i~v~~~~~~----------------------------------------------------------------  210 (676)
                      ..+.|+.|.|......                                                                
T Consensus        75 ~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (282)
T 3pgw_A           75 FPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIM  154 (282)
T ss_pred             CeeCCcEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCccccccccc
Confidence            9999999987532110                                                                


Q ss_pred             -----------------------------------------------CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCce
Q 005812          211 -----------------------------------------------GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLV  243 (676)
Q Consensus       211 -----------------------------------------------~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i  243 (676)
                                                                     ......++|||+|||..+++++|+++|+.||.|
T Consensus       155 ~~~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i  234 (282)
T 3pgw_A          155 HHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGF  234 (282)
T ss_pred             ccCCCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCe
Confidence                                                           011245789999999999999999999999999


Q ss_pred             EEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC-CeeEEEEEec
Q 005812          244 WNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG-KRPIAVDWAV  294 (676)
Q Consensus       244 ~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~-g~~i~v~~a~  294 (676)
                      .+|+++.+     .+|||||+|.+.++|.+|++.|||..|. |+.|+|.|++
T Consensus       235 ~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          235 KEVRLVPG-----RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EEEEEecC-----CCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            99999875     3589999999999999999999999999 9999999985

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

Probab=99.93  E-value=8.5e-26  Score=218.35  Aligned_cols=157  Identities=16%  Similarity=0.233  Sum_probs=139.4

Q ss_pred             CcEEEEcCCCc-cccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecC
Q 005812          121 ARTVIIGGLLN-ADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKG  199 (676)
Q Consensus       121 ~~~l~V~nLp~-~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~  199 (676)
                      +++|||+|||+ ++++++|+++|+.||.|.+|.++.++              +|||||+|.+.++|.+|+..|||..+.|
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~--------------~g~afV~f~~~~~a~~A~~~l~~~~~~g   68 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--------------KENALVQMADGNQAQLAMSHLNGHKLHG   68 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC--------------SSCCEEECTTTHHHHHHHHHHTTCCCSS
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC--------------CCEEEEEECCHHHHHHHHHHhCCCeecC
Confidence            57899999999 99999999999999999999977432              7899999999999999999999999999


Q ss_pred             eEEEEecCCCC-----------------------------------CCCCCCcEEEEcCCCCCCCHHHHHHhhccCC-ce
Q 005812          200 GTVWARQLGGE-----------------------------------GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVG-LV  243 (676)
Q Consensus       200 ~~i~v~~~~~~-----------------------------------~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G-~i  243 (676)
                      +.|.+......                                   ....+.++|||+|||..+++++|+++|+.|| .|
T Consensus        69 ~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v  148 (198)
T 1qm9_A           69 KPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVV  148 (198)
T ss_dssp             CCCEEEECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCC
T ss_pred             eEEEEEEecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCc
Confidence            99988533211                                   0113478999999999999999999999999 99


Q ss_pred             EEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC-CeeEEEEEecCC
Q 005812          244 WNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG-KRPIAVDWAVPK  296 (676)
Q Consensus       244 ~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~-g~~i~v~~a~~~  296 (676)
                      ..|.+..+     .+|||||+|.+.++|.+|+..|||..+. |+.|+|.|+.++
T Consensus       149 ~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          149 KGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             CEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             eEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            99999764     4789999999999999999999999999 999999999764

>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

Probab=99.93  E-value=2.4e-25  Score=224.72  Aligned_cols=157  Identities=20%  Similarity=0.206  Sum_probs=142.7

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeec
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIK  198 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~  198 (676)
                      ...++|||+|||+++++++|+++|+.||.|..|.+.               +++|||||+|.+.++|.+|+..|||..+.
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~---------------~~kg~afV~f~~~~~A~~A~~~l~g~~i~   84 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN---------------RDRGFGFIRLESRTLAEIAKAELDGTILK   84 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEE---------------TTTTEEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEe---------------CCCcEEEEEECCHHHHHHHHHHcCCcEEC
Confidence            456799999999999999999999999999999964               34799999999999999999999999999


Q ss_pred             CeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHh
Q 005812          199 GGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF  278 (676)
Q Consensus       199 ~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l  278 (676)
                      |+.|.|....      ...+|||+|||..+++++|+++|+.||.|..|.|+.+ .+|.++|||||+|.+.++|.+|+..|
T Consensus        85 g~~l~v~~a~------~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l  157 (261)
T 3sde_A           85 SRPLRIRFAT------HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERC  157 (261)
T ss_dssp             TEECEEEECC------CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CceeEeeecc------cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHh
Confidence            9999997543      4679999999999999999999999999999999998 58999999999999999999999999


Q ss_pred             C-CceeC---CeeEEEEEecCCC
Q 005812          279 N-GQKFG---KRPIAVDWAVPKN  297 (676)
Q Consensus       279 ~-~~~~~---g~~i~v~~a~~~~  297 (676)
                      + +..+.   +++|.|.++.+..
T Consensus       158 ~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          158 GDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             HHSCEESSSSCCBCEEEECCCEE
T ss_pred             cCCeEEecCCCceEEEeeccccC
Confidence            5 44444   9999999987653

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

Probab=99.83  E-value=5.8e-20  Score=170.39  Aligned_cols=82  Identities=24%  Similarity=0.395  Sum_probs=78.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|+.||.|..|+|+.+..++.++|||||+|.+.++|.+|+..||     |..|+|++|.|
T Consensus        70 ~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l~v  144 (158)
T 2kn4_A           70 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMD-----GAVLDGRELRV  144 (158)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHST-----TEESSSSEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhC-----CCEECCeEEEE
Confidence            5799999999999999999999999999999999998899999999999999999999999999     99999999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .++.++.
T Consensus       145 ~~a~~~~  151 (158)
T 2kn4_A          145 QMARYGR  151 (158)
T ss_dssp             EEECCSS
T ss_pred             EECCCCC
Confidence            9998753

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

Probab=99.83  E-value=4.2e-20  Score=171.29  Aligned_cols=128  Identities=23%  Similarity=0.280  Sum_probs=107.8

Q ss_pred             CccceEEEEeCCHHHHHHHHHHhCCCeecCeEEEEec-------------CCCCCCCCCCcEEEEcCCCCCCCHHHHHHh
Q 005812          170 CKMDASAVLYTTVKSACASVALLHQKEIKGGTVWARQ-------------LGGEGSKTQKWKLIIRNIPFKAKVNEIKDM  236 (676)
Q Consensus       170 ~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~~i~v~~-------------~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~  236 (676)
                      +++|||||+|.+.++|++|+..+++....+....+..             ..........++|||+|||+.+++++|+++
T Consensus        11 ~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~   90 (158)
T 2kn4_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRV   90 (158)
T ss_dssp             SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTCCHHHHHHH
T ss_pred             cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHH
Confidence            6899999999999999999998875432222222110             011223345789999999999999999999


Q ss_pred             hccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCC
Q 005812          237 FSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKN  297 (676)
Q Consensus       237 F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~  297 (676)
                      |+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+.++.
T Consensus        91 F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           91 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             HHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             HHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            9999999999999998899999999999999999999999999999999999999998764

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

Probab=99.81  E-value=7.7e-20  Score=159.51  Aligned_cols=80  Identities=36%  Similarity=0.561  Sum_probs=74.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      ..+|||+|||+.+++++|+++|++||.|.+|+|+.+.  +.++|||||+|.+.++|.+|++.|+     +..|+|+.|.|
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~-----~~~~~g~~i~V   77 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMN-----GMLLNDRKVFV   77 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHT-----TCEETTEECEE
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcC-----CCEECCEEEEE
Confidence            3689999999999999999999999999999999985  4579999999999999999999999     99999999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .++.++.
T Consensus        78 ~~a~~~~   84 (115)
T 4f25_A           78 GRFKSRK   84 (115)
T ss_dssp             EESSCCC
T ss_pred             EECCCcc
Confidence            9988754

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

Probab=99.80  E-value=1.9e-19  Score=157.03  Aligned_cols=81  Identities=26%  Similarity=0.400  Sum_probs=74.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ...+|||+|||+++++++|+++|+.||.|.+|+|+++.  +.++|||||+|.+.++|++|++.|+|..|.|+.|.|.++.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45689999999999999999999999999999999985  4589999999999999999999999999999999999987


Q ss_pred             CCC
Q 005812          295 PKN  297 (676)
Q Consensus       295 ~~~  297 (676)
                      ++.
T Consensus        82 ~~~   84 (115)
T 4f25_A           82 SRK   84 (115)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            653

>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

Probab=99.79  E-value=2.6e-19  Score=164.36  Aligned_cols=77  Identities=23%  Similarity=0.351  Sum_probs=72.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      +.++|||+|||+.+++++|+++|++||.|.+|+++.+     ++|||||+|.+.++|.+|+..||     |..|+|++|.
T Consensus        72 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l~  141 (150)
T 2i2y_A           72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELD-----GRTLCGCRVR  141 (150)
T ss_dssp             TSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHS-----SSCSSSSCCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcC-----CCEECCeEEE
Confidence            4589999999999999999999999999999998765     58999999999999999999999     9999999999


Q ss_pred             EEEccCc
Q 005812          504 VLKALDK  510 (676)
Q Consensus       504 v~~a~~k  510 (676)
                      |.++.++
T Consensus       142 v~~a~~~  148 (150)
T 2i2y_A          142 VELSNGE  148 (150)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9999875

>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

Probab=99.78  E-value=4.4e-19  Score=162.81  Aligned_cols=123  Identities=18%  Similarity=0.258  Sum_probs=109.7

Q ss_pred             CCccceEEEEeCCHHHHHHHHHHh-CCCeecCeEEEEecCCC----------------CCCCCCCcEEEEcCCCCCCCHH
Q 005812          169 GCKMDASAVLYTTVKSACASVALL-HQKEIKGGTVWARQLGG----------------EGSKTQKWKLIIRNIPFKAKVN  231 (676)
Q Consensus       169 g~~~g~afV~F~~~~~A~~A~~~l-~~~~~~~~~i~v~~~~~----------------~~~~~~~~~v~V~nLp~~~~e~  231 (676)
                      .+-+|+++|+|.+.++|++|+..+ |+..+.| .+.+.....                .......++|||+|||+.++++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~   88 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKT   88 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCH
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHH
Confidence            356899999999999999999999 9999999 887764332                2234567999999999999999


Q ss_pred             HHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCC
Q 005812          232 EIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKN  297 (676)
Q Consensus       232 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~  297 (676)
                      +|+++|+.||.|.+|.++.+     ++|||||+|.+.++|..|+..|||..|.|+.|+|.|+.++.
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            99999999999999999986     68999999999999999999999999999999999997753

>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}

Probab=99.78  E-value=7.6e-19  Score=148.48  Aligned_cols=81  Identities=25%  Similarity=0.416  Sum_probs=78.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      .+++|||+|||+++|+++|+++|++||.|.+|++++++.+|.++|||||+|.+.++|.+|++.||     |..|+|++|.
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~ln-----g~~~~gr~l~   92 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLN-----GLRLQSKTIK   92 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHT-----TCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhC-----CCEECCEEEE
Confidence            36899999999999999999999999999999999999999999999999999999999999999     9999999999


Q ss_pred             EEEccC
Q 005812          504 VLKALD  509 (676)
Q Consensus       504 v~~a~~  509 (676)
                      |.||+|
T Consensus        93 V~~AkP   98 (99)
T 4fxv_A           93 VSYARP   98 (99)
T ss_dssp             EEECCB
T ss_pred             EEEeeC
Confidence            999875

>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}

Probab=99.77  E-value=1.5e-18  Score=146.62  Aligned_cols=83  Identities=30%  Similarity=0.526  Sum_probs=79.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|++++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|+|.|
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q 005812          293 AVP  295 (676)
Q Consensus       293 a~~  295 (676)
                      |+|
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            976

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

Probab=99.74  E-value=1.2e-17  Score=143.86  Aligned_cols=86  Identities=15%  Similarity=0.162  Sum_probs=80.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      +.++|||+|||+.+++++|+++|++||.|.+|.|+.++.++.++|||||+|.+.++|.+|++.||     |..|+|+.|.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~ln-----g~~~~gr~i~   79 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLH-----LTSVMGNIIH   79 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-----TCEETTEECE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhC-----CCEECCeEEE
Confidence            45899999999999999999999999999999999999999999999999999999999999999     9999999999


Q ss_pred             EEEccCchhhh
Q 005812          504 VLKALDKKLAH  514 (676)
Q Consensus       504 v~~a~~k~~~~  514 (676)
                      |.++..+....
T Consensus        80 V~~a~~~~~~~   90 (110)
T 3s8s_A           80 AQLDIKGQQRM   90 (110)
T ss_dssp             EEECSTTHHHH
T ss_pred             EEECCCCcHHH
Confidence            99997765443

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.74  E-value=1.8e-18  Score=143.86  Aligned_cols=82  Identities=15%  Similarity=0.321  Sum_probs=76.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCC-ceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFG-EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G-~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      ++|||+|||+++|+++|+++|++|| .|.+|+|++++.++.++|||||+|.+.++|.+|++.++    ++..|+||+|.|
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~----~~~~~~gr~i~V   77 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQ----HSLNILGQKVSM   77 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTT----TEEEETTEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcC----CCeEECCEEEEE
Confidence            6899999999999999999999999 89999999999999999999999999999999999874    067899999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .+|.+++
T Consensus        78 ~~a~~~~   84 (91)
T 2lxi_A           78 HYSDPKP   84 (91)
T ss_dssp             ECCCSCC
T ss_pred             EEcCCCC
Confidence            9998764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.72  E-value=7.7e-18  Score=140.56  Aligned_cols=79  Identities=15%  Similarity=0.255  Sum_probs=74.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCc--eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCe----eecC
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGE--VVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGI----FLKG  499 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~--v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~----~l~g  499 (676)
                      .+|||+|||+.+|+++|+++|++||.  +..|++++|+.++.++|||||+|.+.++|.+|++.||     +.    .|+|
T Consensus        10 ~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~ln-----g~~~~~~i~G   84 (95)
T 2lkz_A           10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQ-----SLHPPLKIDG   84 (95)
T ss_dssp             CEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHH-----SSSSCEEETT
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhc-----CCCCCceECC
Confidence            69999999999999999999999995  6789999999999999999999999999999999999     64    6999


Q ss_pred             cEEEEEEccC
Q 005812          500 RQLTVLKALD  509 (676)
Q Consensus       500 r~l~v~~a~~  509 (676)
                      |+|.|.||++
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999875

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.71  E-value=6.4e-18  Score=140.50  Aligned_cols=82  Identities=23%  Similarity=0.405  Sum_probs=76.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCC-ceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhC-CceeCCeeEEEEEe
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVG-LVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN-GQKFGKRPIAVDWA  293 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G-~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-~~~~~g~~i~v~~a  293 (676)
                      +++|||+|||+++|+++|+++|++|| .|.+|+|++++.+|.++|||||+|.+.++|.+|++.++ +..+.|+.|.|.|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            36899999999999999999999999 79999999999999999999999999999999999874 56799999999999


Q ss_pred             cCCC
Q 005812          294 VPKN  297 (676)
Q Consensus       294 ~~~~  297 (676)
                      .|+.
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            8765

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

Probab=99.71  E-value=5e-17  Score=139.99  Aligned_cols=83  Identities=19%  Similarity=0.151  Sum_probs=79.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      .+.++|||+|||+.+++++|+++|++||.|.+|.|++++.+++++|||||+|.+.++|++|++.|||..|.|+.|.|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q 005812          294 VPK  296 (676)
Q Consensus       294 ~~~  296 (676)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            654

>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}

Probab=99.71  E-value=3.8e-17  Score=134.80  Aligned_cols=82  Identities=26%  Similarity=0.381  Sum_probs=76.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      +.++|||+|||..+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+|+..||     +..++|+.|.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~l~   79 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMG-----GQWLGGRQIR   79 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-----TCEETTEECE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcC-----CCEECCeEEE
Confidence            45799999999999999999999999999999999998899999999999999999999999999     9999999999


Q ss_pred             EEEccCc
Q 005812          504 VLKALDK  510 (676)
Q Consensus       504 v~~a~~k  510 (676)
                      |.++.++
T Consensus        80 v~~a~~k   86 (87)
T 3bs9_A           80 TNWATRK   86 (87)
T ss_dssp             EEEEC--
T ss_pred             EEecCCC
Confidence            9999875

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.71  E-value=2.3e-17  Score=137.65  Aligned_cols=84  Identities=29%  Similarity=0.422  Sum_probs=77.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCc--eEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCc----eeCC
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGL--VWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQ----KFGK  285 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~--i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~----~~~g  285 (676)
                      ....-.+|||+|||+.+|+++|+++|++||.  |.+|++++++.+|+++|||||+|.+.++|.+|++.|||.    .+.|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            3445679999999999999999999999995  678999999999999999999999999999999999997    4899


Q ss_pred             eeEEEEEecC
Q 005812          286 RPIAVDWAVP  295 (676)
Q Consensus       286 ~~i~v~~a~~  295 (676)
                      ++|.|+||+.
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999864

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

Probab=99.70  E-value=9.3e-18  Score=150.49  Aligned_cols=123  Identities=24%  Similarity=0.314  Sum_probs=83.0

Q ss_pred             eEEEEeCCHHHHHHHHHHhCCCeecCeEEEEecCCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCC
Q 005812          174 ASAVLYTTVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTD  253 (676)
Q Consensus       174 ~afV~F~~~~~A~~A~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~  253 (676)
                      ++|++|.+...+..|+..+++....|+.... ....+......++|||+|||+.+++++|+++|+.||.|..|.|+.++.
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~~~-~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~   84 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGSMS-YGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY   84 (135)
T ss_dssp             -----------------------------CC-SCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSS
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCCCC-cCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC
Confidence            5788888999999999998887666553221 222233445678999999999999999999999999999999999988


Q ss_pred             CCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCC
Q 005812          254 TGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKN  297 (676)
Q Consensus       254 ~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~  297 (676)
                      ++.++|||||+|.+.++|++|+..|+|..|.|+.|.|.|+.+..
T Consensus        85 ~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A           85 TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  128 (135)
T ss_dssp             SSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCC
T ss_pred             CCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            99999999999999999999999999999999999999998754

>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

Probab=99.70  E-value=6.5e-17  Score=132.11  Aligned_cols=81  Identities=25%  Similarity=0.400  Sum_probs=77.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      .+|||+|||+.+++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|.+|+..||     |..|+|++|.|.
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~-----g~~~~g~~l~v~   76 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ-----GQDLNGRPLRIN   76 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHT-----TCEETTEECEEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhc-----CCeeCCcEEEEE
Confidence            589999999999999999999999999999999998899999999999999999999999999     999999999999


Q ss_pred             EccCch
Q 005812          506 KALDKK  511 (676)
Q Consensus       506 ~a~~k~  511 (676)
                      ++.+++
T Consensus        77 ~a~~~~   82 (83)
T 3md1_A           77 WAAKLE   82 (83)
T ss_dssp             ECCCCC
T ss_pred             ecCcCC
Confidence            998763

>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}

Probab=99.69  E-value=9.7e-17  Score=132.37  Aligned_cols=83  Identities=33%  Similarity=0.575  Sum_probs=77.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      .+.++|||+|||.++++++|+++|+.||.|.+|.++.++.++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.|+
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCC
Q 005812          294 VPK  296 (676)
Q Consensus       294 ~~~  296 (676)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            764

>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

Probab=99.69  E-value=1.3e-16  Score=130.25  Aligned_cols=81  Identities=23%  Similarity=0.535  Sum_probs=77.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      .+|||+|||..+++++|+++|+.||.|.++.++.++.++.++|||||+|.+.++|++|+..|||..+.|+.|+|.|+.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            58999999999999999999999999999999999889999999999999999999999999999999999999999875


Q ss_pred             C
Q 005812          297 N  297 (676)
Q Consensus       297 ~  297 (676)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.69  E-value=1.6e-16  Score=133.39  Aligned_cols=84  Identities=21%  Similarity=0.405  Sum_probs=79.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~   85 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN-----GMELDGR   85 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHT-----TEEETTE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhC-----CCEECCE
Confidence            34456899999999999999999999999999999999998889999999999999999999999999     9999999


Q ss_pred             EEEEEEccC
Q 005812          501 QLTVLKALD  509 (676)
Q Consensus       501 ~l~v~~a~~  509 (676)
                      +|.|.++.+
T Consensus        86 ~l~v~~a~~   94 (95)
T 2cqc_A           86 RIRVSGPSS   94 (95)
T ss_dssp             EEEEECCSC
T ss_pred             EEEEEecCC
Confidence            999999864

>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

Probab=99.69  E-value=1.9e-16  Score=134.09  Aligned_cols=87  Identities=26%  Similarity=0.395  Sum_probs=82.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (99)
T 1whw_A            4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      ++.++..
T Consensus        84 ~a~~~~~   90 (99)
T 1whw_A           84 PSTIKKE   90 (99)
T ss_dssp             ECCCCST
T ss_pred             EcCCCcc
Confidence            9988754

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

Probab=99.69  E-value=1.3e-16  Score=134.23  Aligned_cols=85  Identities=22%  Similarity=0.430  Sum_probs=80.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      +++|||+|||..+++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|.+|++.||     |..|+|+.|.|
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~-----g~~~~g~~l~V   76 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLN-----GYQLGSRFLKC   76 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHT-----TCEETTEECEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhC-----CCeECCeEEEE
Confidence            5799999999999999999999999999999999998889999999999999999999999999     99999999999


Q ss_pred             EEccCchhhh
Q 005812          505 LKALDKKLAH  514 (676)
Q Consensus       505 ~~a~~k~~~~  514 (676)
                      .++.++....
T Consensus        77 ~~a~~~~~~~   86 (96)
T 2x1f_A           77 GYSSNSDISG   86 (96)
T ss_dssp             EECSCSSGGG
T ss_pred             EEcCCCCCCC
Confidence            9999876543

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

Probab=99.69  E-value=1.9e-16  Score=134.35  Aligned_cols=85  Identities=24%  Similarity=0.400  Sum_probs=79.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|.++.+. ++.++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~   86 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMD-----GMTIKEN   86 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHT-----TEESSSC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhC-----CCEECCE
Confidence            34456899999999999999999999999999999999987 89999999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      +|.|.++.++.
T Consensus        87 ~l~v~~a~~~~   97 (100)
T 2do4_A           87 IIKVAISNSGP   97 (100)
T ss_dssp             EEEEEECCCCS
T ss_pred             EEEEEECCCCC
Confidence            99999998764

>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

Probab=99.69  E-value=1.7e-16  Score=138.42  Aligned_cols=86  Identities=27%  Similarity=0.411  Sum_probs=80.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|+|+.++.++.++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~   95 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMN-----GFQIGMK   95 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHT-----TCEETTE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcC-----CCEECCE
Confidence            44456899999999999999999999999999999999998889999999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        96 ~l~V~~a~~~~  106 (115)
T 2cpz_A           96 RLKVQLKRSKN  106 (115)
T ss_dssp             ECEEECCCCSC
T ss_pred             EEEEEEcCCCC
Confidence            99999998764

>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*

Probab=99.69  E-value=1e-16  Score=131.60  Aligned_cols=81  Identities=23%  Similarity=0.389  Sum_probs=77.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+|++.||     |..|+|++|
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l   79 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN-----ESELFGRTI   79 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHT-----TCEETTEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhC-----CCEECCcEE
Confidence            346899999999999999999999999999999999998899999999999999999999999999     999999999


Q ss_pred             EEEEcc
Q 005812          503 TVLKAL  508 (676)
Q Consensus       503 ~v~~a~  508 (676)
                      .|.+|+
T Consensus        80 ~v~~ak   85 (85)
T 3mdf_A           80 RVNLAK   85 (85)
T ss_dssp             EEEECC
T ss_pred             EEEEcC
Confidence            999974

>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

Probab=99.68  E-value=1.4e-16  Score=134.89  Aligned_cols=84  Identities=31%  Similarity=0.497  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .+.++|||+|||+.+++++|+++|+.||.|..|.++.+..++.++|||||+|.+.++|.+|+..||     +..|+|+.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l   80 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVD-----GQVFQGRML   80 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTT-----TEESSSCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhC-----CCEECCcEE
Confidence            346899999999999999999999999999999999998889999999999999999999999999     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        81 ~V~~a~~~~   89 (99)
T 1whw_A           81 HVLPSTIKK   89 (99)
T ss_dssp             EEEECCCCS
T ss_pred             EEEEcCCCc
Confidence            999998865

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

Probab=99.68  E-value=2e-17  Score=140.21  Aligned_cols=84  Identities=19%  Similarity=0.236  Sum_probs=79.6

Q ss_pred             CCCeEEEcCCCC------CCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee
Q 005812          424 LQNTIFICNLPF------DLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL  497 (676)
Q Consensus       424 ~~~~l~V~nLp~------~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l  497 (676)
                      .+++|||+|||+      .+++++|+++|++||.|.+|+|++++.++.++|||||+|.+.++|.+|+..||     |..|
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~ln-----g~~~   79 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH-----GKRL   79 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHT-----TCBS
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhC-----Cccc
Confidence            358999999999      99999999999999999999999999899999999999999999999999999     9999


Q ss_pred             cC-cEEEEEEccCchh
Q 005812          498 KG-RQLTVLKALDKKL  512 (676)
Q Consensus       498 ~g-r~l~v~~a~~k~~  512 (676)
                      .| |.|.|.++.+++.
T Consensus        80 ~g~r~l~V~~a~~~~~   95 (100)
T 3ns6_A           80 DLKHRLFLYTMKDVER   95 (100)
T ss_dssp             SSSCBCEEEESHHHHH
T ss_pred             CCCeEEEEEECchhhh
Confidence            99 9999999987653

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

Probab=99.68  E-value=3.2e-16  Score=133.71  Aligned_cols=87  Identities=26%  Similarity=0.565  Sum_probs=82.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45667999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus        91 ~a~~~~~   97 (103)
T 2cq0_A           91 WAKPSTN   97 (103)
T ss_dssp             ESSCCCC
T ss_pred             ECCCCCC
Confidence            9987653

>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*

Probab=99.68  E-value=1.8e-16  Score=130.11  Aligned_cols=82  Identities=29%  Similarity=0.430  Sum_probs=78.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ..+.++|||+|||+++++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.|
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ec
Q 005812          293 AV  294 (676)
Q Consensus       293 a~  294 (676)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

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

Probab=99.67  E-value=3.5e-16  Score=136.37  Aligned_cols=86  Identities=27%  Similarity=0.407  Sum_probs=80.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~   85 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMG-----GQWLGGR   85 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTT-----TCEETTE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhC-----CCEECCE
Confidence            34456899999999999999999999999999999999998899999999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        86 ~l~V~~a~~~~   96 (115)
T 2dgo_A           86 QIRTNWATRKP   96 (115)
T ss_dssp             ECEEEESSCCC
T ss_pred             EEEEEEccCCC
Confidence            99999998764

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

Probab=99.67  E-value=2.3e-16  Score=134.66  Aligned_cols=86  Identities=23%  Similarity=0.298  Sum_probs=80.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~   85 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVS-----GFGYDHL   85 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTT-----TCEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcC-----CCeeCCc
Confidence            34456899999999999999999999999999999999998899999999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        86 ~l~v~~a~~~~   96 (103)
T 2cq0_A           86 ILNVEWAKPST   96 (103)
T ss_dssp             ECEEEESSCCC
T ss_pred             EEEEEECCCCC
Confidence            99999998764

>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

Probab=99.67  E-value=1.8e-16  Score=135.82  Aligned_cols=86  Identities=26%  Similarity=0.297  Sum_probs=80.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.++.+..++.++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~   85 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMD-----MIKLYGK   85 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSS-----SCBCSSC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhC-----CCeECCe
Confidence            34456899999999999999999999999999999999998889999999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        86 ~l~v~~a~~~~   96 (105)
T 1x5u_A           86 PIRVNKASAHN   96 (105)
T ss_dssp             BCEEEETTTTS
T ss_pred             EEEEEECCCCC
Confidence            99999998764

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

Probab=99.67  E-value=1.9e-16  Score=136.19  Aligned_cols=86  Identities=24%  Similarity=0.453  Sum_probs=80.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|++.|+     |..|+|+
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~-----g~~i~g~   96 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLN-----GFELAGR   96 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHT-----TCCSSSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcC-----CCEECCE
Confidence            34456899999999999999999999999999999999998899999999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        97 ~l~V~~a~~k~  107 (108)
T 2jrs_A           97 PMKVGHVTERT  107 (108)
T ss_dssp             CCEEECSCSSC
T ss_pred             EEEEEEcccCC
Confidence            99999998763

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

Probab=99.67  E-value=2.6e-16  Score=132.41  Aligned_cols=83  Identities=29%  Similarity=0.520  Sum_probs=79.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      .++|||+|||..+++++|+++|+.||.|.+|.++.++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.|+.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            57999999999999999999999999999999999988899999999999999999999999999999999999999987


Q ss_pred             CCC
Q 005812          296 KNI  298 (676)
Q Consensus       296 ~~~  298 (676)
                      +..
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            654

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

Probab=99.67  E-value=2.1e-17  Score=148.19  Aligned_cols=83  Identities=24%  Similarity=0.373  Sum_probs=78.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      +.++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+..||     +..|+|++|.
T Consensus        46 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~-----g~~i~g~~l~  120 (135)
T 2lea_A           46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMD-----GAVLDGRELR  120 (135)
T ss_dssp             GCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTT-----TCCSSSSCCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcC-----CCEECCEEEE
Confidence            35799999999999999999999999999999999998889999999999999999999999999     9999999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.++.++.
T Consensus       121 V~~a~~~~  128 (135)
T 2lea_A          121 VQMARYGR  128 (135)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99998653

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

Probab=99.67  E-value=1.8e-16  Score=133.13  Aligned_cols=83  Identities=25%  Similarity=0.459  Sum_probs=79.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      ++++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|+..||     +..|+|++|.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l~   78 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLN-----GFELAGRPMR   78 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHT-----TCCSSSSCCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhC-----CCeeCCcEEE
Confidence            35899999999999999999999999999999999998889999999999999999999999999     9999999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.++.++.
T Consensus        79 V~~a~~~~   86 (95)
T 2dnz_A           79 VGHVTERL   86 (95)
T ss_dssp             EEESSCCC
T ss_pred             EEEccccc
Confidence            99998764

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

Probab=99.67  E-value=3e-16  Score=131.51  Aligned_cols=82  Identities=28%  Similarity=0.482  Sum_probs=77.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|++.||     +..|+|++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~   87 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAIN-----NKQLFGRV   87 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTT-----TEEETTEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcC-----CCeeCCcE
Confidence            3456899999999999999999999999999999999998889999999999999999999999999     99999999


Q ss_pred             EEEEEcc
Q 005812          502 LTVLKAL  508 (676)
Q Consensus       502 l~v~~a~  508 (676)
                      |.|.+|+
T Consensus        88 l~v~~ak   94 (94)
T 2e5h_A           88 IKASIAI   94 (94)
T ss_dssp             EEEEECC
T ss_pred             EEEEecC
Confidence            9999974

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

Probab=99.67  E-value=1.7e-16  Score=136.26  Aligned_cols=85  Identities=20%  Similarity=0.310  Sum_probs=80.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..++++|||+|||+.+++++|+++|+.||.|..|.++.+..++.++|||||+|.+.++|.+|+..||     |..|+|+.
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~   94 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN-----GQDLMGQP   94 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHT-----TCBSSSSB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhc-----CCEECCcE
Confidence            3456899999999999999999999999999999999998899999999999999999999999999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        95 l~V~~a~~~~  104 (106)
T 1p27_B           95 ISVDWCFVRG  104 (106)
T ss_dssp             CEEEESEESS
T ss_pred             EEEEeecCCC
Confidence            9999987653

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

Probab=99.67  E-value=5.2e-16  Score=131.34  Aligned_cols=86  Identities=20%  Similarity=0.420  Sum_probs=80.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|++ |++..|.|+.|.|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999 99999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      ++.++..
T Consensus        85 ~a~~~~~   91 (99)
T 2dgs_A           85 RAEPRDS   91 (99)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCcc
Confidence            9987654

>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

Probab=99.67  E-value=2.2e-16  Score=147.10  Aligned_cols=122  Identities=24%  Similarity=0.397  Sum_probs=80.6

Q ss_pred             EEeCCHHHHHHHHHHhCCCeec--CeEEEEec--------------------CCCCCCCCCCcEEEEcCCCCCCCHHHHH
Q 005812          177 VLYTTVKSACASVALLHQKEIK--GGTVWARQ--------------------LGGEGSKTQKWKLIIRNIPFKAKVNEIK  234 (676)
Q Consensus       177 V~F~~~~~A~~A~~~l~~~~~~--~~~i~v~~--------------------~~~~~~~~~~~~v~V~nLp~~~~e~~l~  234 (676)
                      .+|.+.++|..|+..+++....  |+......                    ...+......++|||+|||+.+++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            6789999999999988876554  33222210                    0112234456899999999999999999


Q ss_pred             HhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCCC
Q 005812          235 DMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNI  298 (676)
Q Consensus       235 ~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~  298 (676)
                      .+|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.|+.++..
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            9999999999999999988999999999999999999999999999999999999999977643

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

Probab=99.67  E-value=3.6e-16  Score=131.24  Aligned_cols=85  Identities=25%  Similarity=0.484  Sum_probs=80.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ...++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|+|.|+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            45689999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 005812          294 VPKNI  298 (676)
Q Consensus       294 ~~~~~  298 (676)
                      .++..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87653

>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

Probab=99.67  E-value=4.9e-17  Score=135.03  Aligned_cols=81  Identities=12%  Similarity=0.206  Sum_probs=72.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCC--ceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFG--EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G--~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      .+|||+|||+.+++++|+++|++||  .|.+++++.++.+|.++|||||+|.+.++|.+|++.||     |..|+|+.|.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~-----g~~~~gr~i~   76 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLP-----KRELHGQNPV   76 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGG-----GSCSSSCCCE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcC-----CCeeCCEEEE
Confidence            4899999999999999999999999  99999999999899999999999999999999999999     9999999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.++.++.
T Consensus        77 V~~~~~~~   84 (90)
T 3p5t_L           77 VTPSNKLE   84 (90)
T ss_dssp             ECCC----
T ss_pred             EEECCCCc
Confidence            99988764

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

Probab=99.67  E-value=4.8e-16  Score=131.86  Aligned_cols=85  Identities=25%  Similarity=0.439  Sum_probs=80.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|+.||.|..|.|+.++ ++.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999987 89999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.++.
T Consensus        92 ~a~~~~   97 (100)
T 2do4_A           92 ISNSGP   97 (100)
T ss_dssp             ECCCCS
T ss_pred             ECCCCC
Confidence            998764

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

Probab=99.66  E-value=9.3e-16  Score=133.70  Aligned_cols=88  Identities=32%  Similarity=0.568  Sum_probs=82.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      ......++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|++|++.|+|..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   89 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34567799999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEecCCCC
Q 005812          291 DWAVPKNI  298 (676)
Q Consensus       291 ~~a~~~~~  298 (676)
                      .|+.++..
T Consensus        90 ~~a~~~~~   97 (115)
T 2dgo_A           90 NWATRKPP   97 (115)
T ss_dssp             EESSCCCC
T ss_pred             EEccCCCC
Confidence            99987654

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

Probab=99.66  E-value=2.4e-16  Score=133.45  Aligned_cols=84  Identities=25%  Similarity=0.476  Sum_probs=79.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|++ |+     +..|+|+.
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~-----~~~~~g~~   80 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MH-----FHDIMGKK   80 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HC-----CCBSSSCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hC-----CCEECCeE
Confidence            3456899999999999999999999999999999999998889999999999999999999998 99     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        81 l~V~~a~~~~   90 (99)
T 2dgs_A           81 VEVKRAEPRD   90 (99)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEECCCCc
Confidence            9999998764

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

Probab=99.66  E-value=3.4e-16  Score=132.51  Aligned_cols=83  Identities=24%  Similarity=0.261  Sum_probs=78.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCC
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS--------FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSG  492 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~--------v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~  492 (676)
                      ...+.++|||+|||+.+++++|+++|++||.|..        ++++.++.++.++|||||+|.+.++|.+|++.||    
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~----   84 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD----   84 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHT----
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhC----
Confidence            3445689999999999999999999999999999        9999998899999999999999999999999999    


Q ss_pred             CCeeecCcEEEEEEcc
Q 005812          493 LGIFLKGRQLTVLKAL  508 (676)
Q Consensus       493 ~g~~l~gr~l~v~~a~  508 (676)
                       |..|+|+.|.|.+|.
T Consensus        85 -g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           85 -GKEFSGNPIKVSFAT   99 (99)
T ss_dssp             -TCBSSSSBCEEEECC
T ss_pred             -CCEeCCcEEEEEecC
Confidence             999999999999973

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

Probab=99.66  E-value=4.1e-16  Score=130.92  Aligned_cols=84  Identities=25%  Similarity=0.357  Sum_probs=79.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|+.||.|..|.++.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS   90 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             EecC
Q 005812          292 WAVP  295 (676)
Q Consensus       292 ~a~~  295 (676)
                      |+.+
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9864

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

Probab=99.66  E-value=1.7e-16  Score=133.54  Aligned_cols=83  Identities=33%  Similarity=0.462  Sum_probs=78.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSF-VPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v-~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      ++++|||+|||+.+++++|+++|+.||.|..+ +|+.++.++.++|||||+|.+.++|.+|+..||     +..|+|++|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~l   78 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN-----GQYLCNRPI   78 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTT-----TCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcC-----CCEECCEEE
Confidence            35899999999999999999999999999999 999998899999999999999999999999999     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        79 ~v~~a~~~~   87 (96)
T 1x5t_A           79 TVSYAFKKD   87 (96)
T ss_dssp             EEEESCCCC
T ss_pred             EEEEecccC
Confidence            999998764

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

Probab=99.66  E-value=9.2e-17  Score=136.47  Aligned_cols=82  Identities=24%  Similarity=0.317  Sum_probs=75.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ....++|||+|||+++|+++|+++|++||.|.+|.++.+.. +.++|||||+|.+.++|.+|+. ++     +..|+|+.
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~-----~~~~~gr~   80 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TP-----GQKYKETD   80 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SS-----CCCCTTTT
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cC-----CCEECCEE
Confidence            34468999999999999999999999999999999999876 9999999999999999999998 89     99999999


Q ss_pred             EEEEEccCc
Q 005812          502 LTVLKALDK  510 (676)
Q Consensus       502 l~v~~a~~k  510 (676)
                      |.|.++..-
T Consensus        81 l~V~~~~~~   89 (103)
T 1s79_A           81 LLILFKDDY   89 (103)
T ss_dssp             CEEEEHHHH
T ss_pred             EEEEEchHH
Confidence            999997653

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

Probab=99.66  E-value=1.8e-16  Score=135.02  Aligned_cols=84  Identities=23%  Similarity=0.377  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .+.++|||+|||+.+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|.+|++.||     +..|+|+.|
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~l   84 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN-----ESELFGRTI   84 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHT-----TEEETTEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhC-----CCEECCcEE
Confidence            346899999999999999999999999999999999998889999999999999999999999999     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        85 ~V~~a~~~~   93 (102)
T 2cqb_A           85 RVNLAKPMR   93 (102)
T ss_dssp             EEEECCCCC
T ss_pred             EEEeCCCCC
Confidence            999998764

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

Probab=99.66  E-value=3.8e-16  Score=134.26  Aligned_cols=86  Identities=22%  Similarity=0.506  Sum_probs=81.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|+|..|.|+.|+|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      ++.++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            997753

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

Probab=99.66  E-value=3.6e-16  Score=133.12  Aligned_cols=87  Identities=30%  Similarity=0.440  Sum_probs=82.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            45577899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus        88 ~a~~~~~   94 (102)
T 2cqb_A           88 LAKPMRI   94 (102)
T ss_dssp             ECCCCCC
T ss_pred             eCCCCCC
Confidence            9987654

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

Probab=99.66  E-value=3.8e-16  Score=130.84  Aligned_cols=83  Identities=30%  Similarity=0.411  Sum_probs=78.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|++.||+..|.|+.|+|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             Eec
Q 005812          292 WAV  294 (676)
Q Consensus       292 ~a~  294 (676)
                      |++
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            974

>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*

Probab=99.66  E-value=2.6e-16  Score=136.02  Aligned_cols=86  Identities=21%  Similarity=0.314  Sum_probs=80.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...++++|||+|||+.+++++|+++|+.||.|..|.++.+..++.++|||||+|.+.++|.+|+..||     |..|+|+
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~-----g~~~~g~   96 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN-----GAEIMGQ   96 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHT-----TCEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcC-----CCEECCc
Confidence            34456899999999999999999999999999999999998899999999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        97 ~l~V~~a~~~~  107 (110)
T 1oo0_B           97 TIQVDWCFVKG  107 (110)
T ss_dssp             ECEEEESEESS
T ss_pred             EEEEEEcccCC
Confidence            99999988653

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

Probab=99.66  E-value=2.8e-16  Score=130.89  Aligned_cols=80  Identities=18%  Similarity=0.235  Sum_probs=71.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCe--eec
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGI--FLK  498 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~--~l~  498 (676)
                      ...++++|||+|||+++++++|+++|++||.|.+|++++      ++|||||+|.+.++|.+|+..|+     +.  .|.
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln-----~~~~~i~   85 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAA-----DNQIYIA   85 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHH-----HSCEEET
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhc-----CCCceeC
Confidence            344678999999999999999999999999999998874      37899999999999999999998     54  589


Q ss_pred             CcEEEEEEccCch
Q 005812          499 GRQLTVLKALDKK  511 (676)
Q Consensus       499 gr~l~v~~a~~k~  511 (676)
                      ||+|.|.++.+++
T Consensus        86 Gr~i~V~~S~~k~   98 (100)
T 3r27_A           86 GHPAFVNYSTSQK   98 (100)
T ss_dssp             TEEEEEEECSCSC
T ss_pred             CcEEEEEeccccc
Confidence            9999999998753

>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

Probab=99.66  E-value=4.2e-16  Score=133.52  Aligned_cols=88  Identities=26%  Similarity=0.385  Sum_probs=82.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      ......++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|+..|++..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34567799999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEecCCCC
Q 005812          291 DWAVPKNI  298 (676)
Q Consensus       291 ~~a~~~~~  298 (676)
                      .|+.++..
T Consensus        90 ~~a~~~~~   97 (105)
T 1x5u_A           90 NKASAHNK   97 (105)
T ss_dssp             EETTTTSC
T ss_pred             EECCCCCc
Confidence            99987653

>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

Probab=99.66  E-value=7.5e-17  Score=133.89  Aligned_cols=81  Identities=16%  Similarity=0.236  Sum_probs=72.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCC--ceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVG--LVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G--~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      .+|||+|||+++++++|+++|+.||  .|.++.++.++.+|+++|||||+|.+.++|.+|++.|||..|.|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999999999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 005812          295 PKN  297 (676)
Q Consensus       295 ~~~  297 (676)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            764

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

Probab=99.66  E-value=5.8e-16  Score=131.05  Aligned_cols=84  Identities=25%  Similarity=0.465  Sum_probs=79.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEE--------EEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCce
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWN--------VYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK  282 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~--------v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~  282 (676)
                      ......++|||+|||.++++++|+++|++||.|..        +.++.++.+|.++|||||+|.+.++|++|++.|||..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            45567799999999999999999999999999999        9999998899999999999999999999999999999


Q ss_pred             eCCeeEEEEEec
Q 005812          283 FGKRPIAVDWAV  294 (676)
Q Consensus       283 ~~g~~i~v~~a~  294 (676)
                      +.|+.|+|.++.
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999973

>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

Probab=99.66  E-value=5.5e-16  Score=132.78  Aligned_cols=84  Identities=25%  Similarity=0.279  Sum_probs=78.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC--
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG--  499 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g--  499 (676)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|.|+.+. ++.++|||||+|.+.++|.+|+..||     +..+.|  
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~-----g~~~~gg~   85 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALH-----GSQTMPGA   85 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHS-----SCCCCTTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHc-----CCccCCCC
Confidence            3456899999999999999999999999999999999987 78999999999999999999999999     999988  


Q ss_pred             -cEEEEEEccCch
Q 005812          500 -RQLTVLKALDKK  511 (676)
Q Consensus       500 -r~l~v~~a~~k~  511 (676)
                       ++|.|.++.++.
T Consensus        86 ~~~l~V~~a~~~~   98 (105)
T 2dnh_A           86 SSSLVVKFADTDK   98 (105)
T ss_dssp             SSCCEEEESCSSC
T ss_pred             CccEEEEECccCc
Confidence             999999998764

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.6e-16  Score=133.86  Aligned_cols=81  Identities=25%  Similarity=0.324  Sum_probs=72.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+++++++|+++|++||.|.+|+|+++      +|||||+|.+.++|.+|++.|+..   +..|.|++
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~---~~~l~Gr~   83 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSV---TPVLRGQP   83 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTS---CCEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccC---CceECCEE
Confidence            345689999999999999999999999999999998854      799999999999999999988611   47999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.+|.++.
T Consensus        84 l~V~~A~~~~   93 (105)
T 1sjq_A           84 IYIQFSNHKE   93 (105)
T ss_dssp             CCBCCCSSSS
T ss_pred             EEEEEcCCCC
Confidence            9999998764

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

Probab=99.66  E-value=3.2e-16  Score=131.82  Aligned_cols=85  Identities=32%  Similarity=0.518  Sum_probs=80.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEE-EEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNV-YIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ...++|||+|||..+++++|+++|+.||.|..+ .|+.++.++.++|||||+|.+.++|++|+..|||..|.|+.|.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            457899999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 005812          293 AVPKNI  298 (676)
Q Consensus       293 a~~~~~  298 (676)
                      +.++..
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            987653

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

Probab=99.66  E-value=2e-16  Score=134.98  Aligned_cols=86  Identities=26%  Similarity=0.347  Sum_probs=80.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~   83 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMD-----GAELDGR   83 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHS-----SCCBTTB
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcC-----CCEECCc
Confidence            34456899999999999999999999999999999999998889999999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        84 ~l~V~~a~~~~   94 (103)
T 2dnm_A           84 ELRVQVARYGR   94 (103)
T ss_dssp             CCEEEECSSCC
T ss_pred             EEEEEECCcCC
Confidence            99999998653

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

Probab=99.65  E-value=4.1e-16  Score=133.81  Aligned_cols=86  Identities=27%  Similarity=0.573  Sum_probs=80.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.++.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            997653

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

Probab=99.65  E-value=2.1e-16  Score=134.67  Aligned_cols=84  Identities=30%  Similarity=0.530  Sum_probs=79.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .+.++|||+|||+.+++++|+++|+.||.|..|.++.+..++.++|||||+|.+.++|.+|++.||     +..|+|++|
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~l   84 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMN-----GKSVDGRQI   84 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHT-----TCCTTSCCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhC-----CCEECCeEE
Confidence            346899999999999999999999999999999999998889999999999999999999999999     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        85 ~v~~a~~~~   93 (102)
T 1x5s_A           85 RVDQAGKSS   93 (102)
T ss_dssp             EEEEEECCC
T ss_pred             EEEECCCCC
Confidence            999998764

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

Probab=99.65  E-value=9.7e-17  Score=135.97  Aligned_cols=83  Identities=23%  Similarity=0.390  Sum_probs=79.0

Q ss_pred             CCcEEEEcCCCC------CCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC-ee
Q 005812          215 QKWKLIIRNIPF------KAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK-RP  287 (676)
Q Consensus       215 ~~~~v~V~nLp~------~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g-~~  287 (676)
                      ..++|||+|||+      .+++++|+++|++||.|.+|.|++++.+|+++|||||+|.+.++|.+|++.|||..|.| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            467999999999      99999999999999999999999999999999999999999999999999999999999 99


Q ss_pred             EEEEEecCCC
Q 005812          288 IAVDWAVPKN  297 (676)
Q Consensus       288 i~v~~a~~~~  297 (676)
                      |.|.++.++.
T Consensus        85 l~V~~a~~~~   94 (100)
T 3ns6_A           85 LFLYTMKDVE   94 (100)
T ss_dssp             CEEEESHHHH
T ss_pred             EEEEECchhh
Confidence            9999997653

>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

Probab=99.65  E-value=5.5e-16  Score=135.14  Aligned_cols=87  Identities=29%  Similarity=0.401  Sum_probs=81.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+++++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|++|++.||+..|.|+.|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34566899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus       101 ~a~~~~~  107 (115)
T 2cpz_A          101 LKRSKND  107 (115)
T ss_dssp             CCCCSCC
T ss_pred             EcCCCCc
Confidence            9987654

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

Probab=99.65  E-value=4.1e-16  Score=134.04  Aligned_cols=86  Identities=28%  Similarity=0.425  Sum_probs=80.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHc-CCCCCCCeeec
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLH-QVTKRPKGTGFLKFKTVEAATAAVSAS-KTTSGLGIFLK  498 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~-~~~~~~~g~afV~F~t~~~A~~Al~~l-~~~~~~g~~l~  498 (676)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|.|+.+ ..++.++|||||+|.+.++|.+|+..| |     +..|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~-----~~~~~   85 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCH-----STHLY   85 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHT-----CCBSS
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhcc-----CCeEC
Confidence            3445689999999999999999999999999999999988 778999999999999999999999999 9     99999


Q ss_pred             CcEEEEEEccCch
Q 005812          499 GRQLTVLKALDKK  511 (676)
Q Consensus       499 gr~l~v~~a~~k~  511 (676)
                      |+.|.|.++.++.
T Consensus        86 g~~l~v~~a~~~~   98 (107)
T 2cph_A           86 GRRLVLEWADSEV   98 (107)
T ss_dssp             SCBCEEEECCCCC
T ss_pred             CCEEEEEeCCCCC
Confidence            9999999998764

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

Probab=99.65  E-value=4.1e-16  Score=133.06  Aligned_cols=87  Identities=28%  Similarity=0.481  Sum_probs=81.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      ......++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            34556789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEecCCC
Q 005812          291 DWAVPKN  297 (676)
Q Consensus       291 ~~a~~~~  297 (676)
                      .|+.+..
T Consensus        88 ~~a~~~~   94 (103)
T 2dnm_A           88 QVARYGR   94 (103)
T ss_dssp             EECSSCC
T ss_pred             EECCcCC
Confidence            9997654

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

Probab=99.65  E-value=3.3e-16  Score=132.35  Aligned_cols=83  Identities=27%  Similarity=0.338  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCC---CCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQV---TKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~---~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      +.++|||+|||+.+++++|+++|+.||.|..|.++.+..   ++.++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~   78 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQ-----GHTVDGH   78 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHST-----TCEETTE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhC-----CCeeCCe
Confidence            357999999999999999999999999999999998876   55889999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        79 ~l~V~~a~~~~   89 (98)
T 2cpf_A           79 KLEVRISERAT   89 (98)
T ss_dssp             ECEEECSSCSS
T ss_pred             EEEEEEccCCC
Confidence            99999998754

>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

Probab=99.65  E-value=8.2e-16  Score=126.73  Aligned_cols=80  Identities=30%  Similarity=0.499  Sum_probs=74.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|++. +     +..|+|+.
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~-----~~~~~g~~   81 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-K-----EHRLDGRV   81 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-S-----CEEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-C-----CCEECCEE
Confidence            34568999999999999999999999999999999999988999999999999999999999965 6     78899999


Q ss_pred             EEEEEc
Q 005812          502 LTVLKA  507 (676)
Q Consensus       502 l~v~~a  507 (676)
                      |.|.+|
T Consensus        82 i~v~~A   87 (87)
T 3s7r_A           82 IDPKKA   87 (87)
T ss_dssp             EEEEEC
T ss_pred             EEEEeC
Confidence            999885

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

Probab=99.65  E-value=9.2e-16  Score=138.61  Aligned_cols=87  Identities=23%  Similarity=0.434  Sum_probs=81.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          420 GEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       420 ~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      ......++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+..||     +..|+|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g  111 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLN-----GFNILN  111 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTT-----TEECSS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhC-----CCEECC
Confidence            345567899999999999999999999999999999999998889999999999999999999999999     999999


Q ss_pred             cEEEEEEccCch
Q 005812          500 RQLTVLKALDKK  511 (676)
Q Consensus       500 r~l~v~~a~~k~  511 (676)
                      +.|.|.++.++.
T Consensus       112 ~~l~v~~a~~~~  123 (139)
T 1u6f_A          112 KRLKVALAASGH  123 (139)
T ss_dssp             CEEEEEESSCCC
T ss_pred             eEEEEEECCCCC
Confidence            999999998764

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

Probab=99.65  E-value=4.7e-16  Score=132.42  Aligned_cols=88  Identities=28%  Similarity=0.457  Sum_probs=82.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      ......++|||+|||+++++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|++.||+..|.|+.|+|
T Consensus         7 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   86 (102)
T 1x5s_A            7 GMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   86 (102)
T ss_dssp             CCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34557789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEecCCCC
Q 005812          291 DWAVPKNI  298 (676)
Q Consensus       291 ~~a~~~~~  298 (676)
                      .|+.++..
T Consensus        87 ~~a~~~~~   94 (102)
T 1x5s_A           87 DQAGKSSD   94 (102)
T ss_dssp             EEEECCCC
T ss_pred             EECCCCCC
Confidence            99987653

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

Probab=99.65  E-value=5.2e-16  Score=130.26  Aligned_cols=82  Identities=27%  Similarity=0.388  Sum_probs=76.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.+.. +.++|||||+|.+.++|.+|+..||     +..|+|++
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~   86 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLN-----GIRLYGRP   86 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHT-----TCEETTEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhC-----CCEECCCE
Confidence            34568999999999999999999999999999999999875 8899999999999999999999999     99999999


Q ss_pred             EEEEEccC
Q 005812          502 LTVLKALD  509 (676)
Q Consensus       502 l~v~~a~~  509 (676)
                      |.|.++.+
T Consensus        87 l~V~~a~~   94 (95)
T 2ywk_A           87 INVSGPSS   94 (95)
T ss_dssp             CEEECCCC
T ss_pred             EEEEEcCC
Confidence            99999763

>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

Probab=99.65  E-value=9.9e-16  Score=132.62  Aligned_cols=87  Identities=26%  Similarity=0.411  Sum_probs=81.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhC------CceeCC
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN------GQKFGK  285 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~------~~~~~g  285 (676)
                      .....++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+..|+      +..|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            44567899999999999999999999999999999999999899999999999999999999999999      999999


Q ss_pred             eeEEEEEecCCCC
Q 005812          286 RPIAVDWAVPKNI  298 (676)
Q Consensus       286 ~~i~v~~a~~~~~  298 (676)
                      +.|.|.|+.++..
T Consensus        91 ~~l~v~~a~~~~~  103 (111)
T 1x4h_A           91 RQLKVDLAVTRDE  103 (111)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCcc
Confidence            9999999987653

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

Probab=99.65  E-value=4.9e-16  Score=124.44  Aligned_cols=72  Identities=24%  Similarity=0.324  Sum_probs=68.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      +..|||+||++.+|+++|+++|.+||+|.++++..      ++|||||+|.++++|.+|++.||     +..++||+|.|
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln-----~~~l~gr~I~V   75 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALN-----NCVLANTTIFA   75 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHT-----TEEETTEEEEE
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhc-----CCEECCcEEEE
Confidence            46899999999999999999999999999998853      69999999999999999999999     99999999999


Q ss_pred             EEc
Q 005812          505 LKA  507 (676)
Q Consensus       505 ~~a  507 (676)
                      .+|
T Consensus        76 ~~A   78 (89)
T 2wbr_A           76 ESP   78 (89)
T ss_dssp             ECC
T ss_pred             EEC
Confidence            998

>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

Probab=99.65  E-value=6.4e-16  Score=128.00  Aligned_cols=80  Identities=21%  Similarity=0.459  Sum_probs=76.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|.+|+ .||     +..|+|+.|.|
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~-----g~~~~g~~l~V   79 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALD-----ESLFRGRQIKV   79 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGT-----TCEETTEECEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcC-----CCEECCcEEEE
Confidence            479999999999999999999999999999999999889999999999999999999999 999     99999999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      .++.++
T Consensus        80 ~~a~~~   85 (89)
T 3ucg_A           80 IPKRTN   85 (89)
T ss_dssp             EETTTT
T ss_pred             EEccCC
Confidence            998764

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

Probab=99.65  E-value=6e-16  Score=142.03  Aligned_cols=84  Identities=14%  Similarity=0.248  Sum_probs=78.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCC--ceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFG--EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G--~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..++|||+|||+.+++++|+++|+.||  .|..|+|+.|+.+|.++|||||+|.+.++|.+|+..||     |..|+|+.
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~ln-----g~~~~Gr~  128 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLP-----GKVLNGEK  128 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHST-----TCEETTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcC-----CCEECCeE
Confidence            357999999999999999999999999  99999999999999999999999999999999999999     99999999


Q ss_pred             EEEEEccCchh
Q 005812          502 LTVLKALDKKL  512 (676)
Q Consensus       502 l~v~~a~~k~~  512 (676)
                      |.|.+|.++..
T Consensus       129 l~V~~a~~~~~  139 (156)
T 3n9u_C          129 VDVRPATRQNL  139 (156)
T ss_dssp             CEEEECCHHHH
T ss_pred             eEEEEcCCCcc
Confidence            99999987653

>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

Probab=99.65  E-value=4.7e-16  Score=144.81  Aligned_cols=85  Identities=21%  Similarity=0.305  Sum_probs=79.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .++++|||+|||+.+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|.+|+..||     |..|.|++|
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~-----g~~~~g~~l  144 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN-----GAEIMGQTI  144 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHT-----TCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhC-----CCEECCEEE
Confidence            346899999999999999999999999999999999998899999999999999999999999999     999999999


Q ss_pred             EEEEccCchh
Q 005812          503 TVLKALDKKL  512 (676)
Q Consensus       503 ~v~~a~~k~~  512 (676)
                      .|.|+.++..
T Consensus       145 ~V~~a~~~~~  154 (165)
T 1rk8_A          145 QVDWCFVKGP  154 (165)
T ss_dssp             EEEESEECC-
T ss_pred             EEEEecCCCC
Confidence            9999987653

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

Probab=99.65  E-value=9e-16  Score=130.90  Aligned_cols=83  Identities=27%  Similarity=0.383  Sum_probs=77.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+.+++++|+++|+.|| |..|.|+.+..++.++|||||+|.+.++|.+|+ .||     +..|+|+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~-----g~~~~g~~   84 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYD-----GALLGDRS   84 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGT-----TCEETTEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhC-----CCeECCeE
Confidence            34468999999999999999999999997 999999999889999999999999999999999 899     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        85 l~V~~a~~~~   94 (103)
T 2dng_A           85 LRVDIAEGRK   94 (103)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEecCCC
Confidence            9999998764

>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

Probab=99.65  E-value=2.6e-16  Score=134.53  Aligned_cols=86  Identities=34%  Similarity=0.534  Sum_probs=80.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      ..++|||+|||+.+++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|.+|++.||     |..|+|+.|.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l~   81 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLN-----GREFSGRALR   81 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSS-----SBSCSSSCBE
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhC-----CCeeCCcEEE
Confidence            35799999999999999999999999999999999998889999999999999999999999999     9999999999


Q ss_pred             EEEccCchhhh
Q 005812          504 VLKALDKKLAH  514 (676)
Q Consensus       504 v~~a~~k~~~~  514 (676)
                      |.++.++....
T Consensus        82 v~~a~~~~~~~   92 (104)
T 1p1t_A           82 VDNAASEKNKE   92 (104)
T ss_dssp             EEETTCTTHHH
T ss_pred             EEeCCCccchh
Confidence            99998876544

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

Probab=99.64  E-value=9.6e-16  Score=131.75  Aligned_cols=87  Identities=34%  Similarity=0.649  Sum_probs=81.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEccc-CCCCCceeEEEEEecCHHHHHHHHHHh-CCceeCCeeEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHN-TDTGLSKGFAFVKFTCKRDAESAIQKF-NGQKFGKRPIA  289 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~-~~~~~~~g~afV~f~~~~~A~~A~~~l-~~~~~~g~~i~  289 (676)
                      .....++|||+|||..+++++|+++|+.||.|..|.|+.+ +.++.++|||||+|.+.++|.+|+..| |+..|.|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            4556789999999999999999999999999999999998 778999999999999999999999999 99999999999


Q ss_pred             EEEecCCCC
Q 005812          290 VDWAVPKNI  298 (676)
Q Consensus       290 v~~a~~~~~  298 (676)
                      |.|+.++..
T Consensus        91 v~~a~~~~~   99 (107)
T 2cph_A           91 LEWADSEVT   99 (107)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999987653

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=3.3e-16  Score=136.28  Aligned_cols=83  Identities=22%  Similarity=0.353  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      ...++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+ .||     +..|+|+.|
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~-----g~~~~g~~l   96 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLT-----GQRLLGVPI   96 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHT-----TEEETTEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcC-----CCEeCCeEE
Confidence            34589999999999999999999999999999999999888999999999999999999999 999     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        97 ~V~~a~~~~  105 (114)
T 2cq4_A           97 IVQASQAEK  105 (114)
T ss_dssp             EEEEHHHHH
T ss_pred             EEEecCCCc
Confidence            999987654

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

Probab=99.64  E-value=6.4e-16  Score=135.40  Aligned_cols=83  Identities=25%  Similarity=0.418  Sum_probs=77.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|.+|++.||     +..|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~  110 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMN-----GFQVGTK  110 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCC-----CCEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcC-----CCEECCE
Confidence            34557899999999999999999999999999999999998889999999999999999999999999     9999999


Q ss_pred             EEEEEEcc
Q 005812          501 QLTVLKAL  508 (676)
Q Consensus       501 ~l~v~~a~  508 (676)
                      .|.|.+++
T Consensus       111 ~l~V~~ak  118 (118)
T 2khc_A          111 RLKVQLKK  118 (118)
T ss_dssp             ECCEEEC-
T ss_pred             EEEEEecC
Confidence            99999974

>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*

Probab=99.64  E-value=6.4e-16  Score=133.55  Aligned_cols=86  Identities=29%  Similarity=0.541  Sum_probs=81.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|+..|+|..|.|+.|.|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.++.
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            997654

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

Probab=99.64  E-value=7e-16  Score=130.57  Aligned_cols=86  Identities=24%  Similarity=0.331  Sum_probs=80.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceE-EEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCee---
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVW-NVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRP---  287 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~-~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~---  287 (676)
                      .....++|||+|||+++++++|+++|++||.|. .|.|++++.++.++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   84 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK   84 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCE
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcce
Confidence            445678999999999999999999999999999 9999999889999999999999999999999999999999999   


Q ss_pred             -EEEEEecCCC
Q 005812          288 -IAVDWAVPKN  297 (676)
Q Consensus       288 -i~v~~a~~~~  297 (676)
                       |+|.|+.+..
T Consensus        85 ~l~v~~a~~~~   95 (99)
T 2div_A           85 RFKLNYATYSG   95 (99)
T ss_dssp             ECCEEETTCCS
T ss_pred             eEEEeecCCCC
Confidence             9999997754

>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

Probab=99.64  E-value=1.5e-15  Score=129.99  Aligned_cols=86  Identities=23%  Similarity=0.401  Sum_probs=79.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC---eeE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK---RPI  288 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g---~~i  288 (676)
                      .....++|||+|||..+++++|+++|+.||.|..|.|+.++ ++.++|||||+|.+.++|.+|++.|||..+.|   +.|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            34567899999999999999999999999999999999987 78999999999999999999999999999988   999


Q ss_pred             EEEEecCCCC
Q 005812          289 AVDWAVPKNI  298 (676)
Q Consensus       289 ~v~~a~~~~~  298 (676)
                      .|.|+.++..
T Consensus        90 ~V~~a~~~~~   99 (105)
T 2dnh_A           90 VVKFADTDKE   99 (105)
T ss_dssp             EEEESCSSCC
T ss_pred             EEEECccCcc
Confidence            9999987653

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

Probab=99.64  E-value=6e-16  Score=130.97  Aligned_cols=83  Identities=20%  Similarity=0.337  Sum_probs=78.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCcee-EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVV-SFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~-~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      .+.++|||+|||+.+++++|+++|++||.|. .|+++.++.++.++|||||+|.+.++|.+|+..||     +..|.|+.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~   81 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKIN-----GKPLPGAT   81 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTT-----TSEESSCS
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHc-----CCccCCCC
Confidence            3468999999999999999999999999999 99999998899999999999999999999999999     99999999


Q ss_pred             ----EEEEEccCc
Q 005812          502 ----LTVLKALDK  510 (676)
Q Consensus       502 ----l~v~~a~~k  510 (676)
                          |.|.||.+.
T Consensus        82 ~~~~l~v~~a~~~   94 (99)
T 2div_A           82 PAKRFKLNYATYS   94 (99)
T ss_dssp             SCEECCEEETTCC
T ss_pred             cceeEEEeecCCC
Confidence                999998764

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

Probab=99.64  E-value=1.4e-15  Score=129.73  Aligned_cols=85  Identities=27%  Similarity=0.443  Sum_probs=79.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|+.||.|..|.|+.+  ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            4456789999999999999999999999999999999987  78899999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus        89 ~a~~~~~   95 (103)
T 2d9p_A           89 LAQRKEE   95 (103)
T ss_dssp             ECSSCCC
T ss_pred             Eeccccc
Confidence            9987653

>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

Probab=99.64  E-value=3e-16  Score=139.31  Aligned_cols=86  Identities=22%  Similarity=0.423  Sum_probs=80.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~ln-----g~~i~g~  116 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN-----GMELDGR  116 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHT-----TCCSSSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhC-----CCEECCE
Confidence            44567899999999999999999999999999999999998889999999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      +|.|.++.++.
T Consensus       117 ~l~V~~a~~~~  127 (129)
T 2kxn_B          117 RIRVDFSITKR  127 (129)
T ss_dssp             CCEESCCSSSS
T ss_pred             EEEEEEecCCC
Confidence            99999988753

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

Probab=99.64  E-value=6.9e-16  Score=131.62  Aligned_cols=83  Identities=30%  Similarity=0.440  Sum_probs=77.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.+  ++.++|||||+|.+.++|.+|+..||     +..|.|+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~   84 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMN-----GRIVATKP   84 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHT-----TCBSSSSB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhC-----CCEeCCcE
Confidence            345689999999999999999999999999999999887  78899999999999999999999999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        85 l~V~~a~~~~   94 (103)
T 2d9p_A           85 LYVALAQRKE   94 (103)
T ss_dssp             CEEEECSSCC
T ss_pred             EEEEEecccc
Confidence            9999998764

>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

Probab=99.64  E-value=1e-15  Score=131.57  Aligned_cols=81  Identities=21%  Similarity=0.386  Sum_probs=76.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..++++|||+|||+.+++++|+++|++||.|..|.|+.+. ++.++|||||+|.+.++|.+|+..||     +..|+|+.
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~   99 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYN-----GVPLDGRP   99 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHT-----TCEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhC-----CCEeCCcE
Confidence            3456899999999999999999999999999999999997 89999999999999999999999999     99999999


Q ss_pred             EEEEEcc
Q 005812          502 LTVLKAL  508 (676)
Q Consensus       502 l~v~~a~  508 (676)
                      |.|.++.
T Consensus       100 l~V~~a~  106 (107)
T 3ulh_A          100 MNIQLVT  106 (107)
T ss_dssp             CEEEEEC
T ss_pred             EEEEEeC
Confidence            9999975

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

Probab=99.64  E-value=1.9e-15  Score=128.89  Aligned_cols=85  Identities=24%  Similarity=0.479  Sum_probs=79.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|+.|| |..|.|+.++.++.++|||||+|.+.++|.+|+ .||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            455678999999999999999999999997 999999999989999999999999999999999 799999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus        89 ~a~~~~~   95 (103)
T 2dng_A           89 IAEGRKQ   95 (103)
T ss_dssp             ECCCCCC
T ss_pred             EecCCCC
Confidence            9987653

>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

Probab=99.64  E-value=6.2e-16  Score=132.16  Aligned_cols=82  Identities=22%  Similarity=0.359  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVT-KRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~-~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      .+.++|||+|||+.+++++|+++|+.|| |..|.|+.+..+ +.++|||||+|.+.++|.+|+ .||     +..|+|+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~-----g~~~~g~~   85 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLN-----EESLGNKR   85 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGG-----TCEETTEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcC-----CCEeCCcE
Confidence            3458999999999999999999999999 999999999877 899999999999999999999 999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        86 l~V~~a~~~~   95 (104)
T 1wi8_A           86 IRVDVADQAQ   95 (104)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEccCCC
Confidence            9999998764

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

Probab=99.64  E-value=8.5e-16  Score=129.77  Aligned_cols=84  Identities=24%  Similarity=0.421  Sum_probs=78.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCC---CCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTD---TGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~---~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      .+.++|||+|||+++++++|+++|+.||.|..|.|+.++.   ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3568999999999999999999999999999999998876   5589999999999999999999999999999999999


Q ss_pred             EEecCCC
Q 005812          291 DWAVPKN  297 (676)
Q Consensus       291 ~~a~~~~  297 (676)
                      .|+.++.
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9997764

>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}

Probab=99.64  E-value=8.3e-16  Score=127.00  Aligned_cols=83  Identities=22%  Similarity=0.346  Sum_probs=77.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCC-ceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGL-SKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~-~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ..++|||+|||.++++++|+++|++||.|.++.++.+..++. ++|||||+|.+.++|.+|++.|||..+.|+.|.|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            457999999999999999999999999999999999877665 8999999999999999999999999999999999999


Q ss_pred             cCCC
Q 005812          294 VPKN  297 (676)
Q Consensus       294 ~~~~  297 (676)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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}

Probab=99.64  E-value=5.7e-16  Score=128.00  Aligned_cols=81  Identities=17%  Similarity=0.362  Sum_probs=76.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCC-cceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKR-PKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~-~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      .++|||+|||+.+++++|+++|++||.|..+.++.+..++. ++|||||+|.+.++|.+|+..||     |..|+|+.|.
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l~   78 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMD-----GGQIDGQEIT   78 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHT-----TCEETTEECE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcC-----CCeECCeEEE
Confidence            47999999999999999999999999999999998876655 89999999999999999999999     9999999999


Q ss_pred             EEEccCc
Q 005812          504 VLKALDK  510 (676)
Q Consensus       504 v~~a~~k  510 (676)
                      |.++.+.
T Consensus        79 v~~a~~~   85 (88)
T 4a8x_A           79 ATAVLAP   85 (88)
T ss_dssp             EEEECCC
T ss_pred             EEECCCC
Confidence            9998764

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

Probab=99.63  E-value=2.3e-15  Score=128.41  Aligned_cols=83  Identities=24%  Similarity=0.281  Sum_probs=76.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.+..  .++|||||+|.+.++|.+|+..||     +..|.|+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~   84 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMN-----GRKILGKE   84 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHT-----TEEETTEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhC-----CCCcCCCe
Confidence            34568999999999999999999999999999999998853  368999999999999999999999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        85 l~V~~a~~~~   94 (103)
T 2cqi_A           85 VKVNWATTPS   94 (103)
T ss_dssp             EEEEECCCTT
T ss_pred             EEEEECCCCc
Confidence            9999998754

>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}

Probab=99.63  E-value=7.2e-16  Score=134.33  Aligned_cols=83  Identities=20%  Similarity=0.370  Sum_probs=78.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.+. ++.++|||||+|.+.++|.+|++.||     |..|+|+.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~-----g~~~~g~~l   78 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMN-----GKSLHGKAI   78 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCS-----SCBCSSSBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhC-----CCEECCEEE
Confidence            345899999999999999999999999999999999987 89999999999999999999999999     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        79 ~V~~a~~~~   87 (116)
T 2fy1_A           79 KVEQAKKPS   87 (116)
T ss_dssp             EEEECCCSS
T ss_pred             EEEECCCCC
Confidence            999998754

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=7.7e-16  Score=131.85  Aligned_cols=85  Identities=24%  Similarity=0.436  Sum_probs=79.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+.. +     +..|+|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~-----~~~~~g~   85 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-R-----PHTLDGR   85 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-C-----SEEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-C-----CCeECCE
Confidence            344568999999999999999999999999999999999988999999999999999999999998 9     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        86 ~l~V~~a~~~~   96 (105)
T 2dh8_A           86 NIDPKPCTPRG   96 (105)
T ss_dssp             EEBCCCSCCSS
T ss_pred             EEEEEEccCCC
Confidence            99999998764

>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

Probab=99.63  E-value=2.5e-16  Score=137.36  Aligned_cols=81  Identities=23%  Similarity=0.402  Sum_probs=74.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||..+++++|+++|+.||.|.+|.++.+   +.++|||||+|.+.++|.+|+..|||..+.|+.|.|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            445689999999999999999999999999999999875   44689999999999999999999999999999999999


Q ss_pred             ecCC
Q 005812          293 AVPK  296 (676)
Q Consensus       293 a~~~  296 (676)
                      +.+.
T Consensus        82 a~~~   85 (115)
T 3lqv_A           82 YNAN   85 (115)
T ss_dssp             CCHH
T ss_pred             ecCC
Confidence            8653

>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

Probab=99.63  E-value=1.9e-15  Score=128.88  Aligned_cols=84  Identities=23%  Similarity=0.498  Sum_probs=77.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|.|+.+..  .++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~   83 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLH-----GTVVEGR   83 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHT-----TCEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhC-----CCEECCE
Confidence            344568999999999999999999999999999999998753  389999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        84 ~l~v~~a~~~~   94 (103)
T 2cq3_A           84 KIEVNNATARV   94 (103)
T ss_dssp             ECEEEECCSSC
T ss_pred             EEEEEEcccCC
Confidence            99999998764

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

Probab=99.63  E-value=7.9e-16  Score=128.20  Aligned_cols=80  Identities=15%  Similarity=0.156  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCce--eCCeeEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK--FGKRPIA  289 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~--~~g~~i~  289 (676)
                      ...++++|||+|||.++++++|+++|++||.|.+|.+++      .+|||||+|.+.++|..|++.|++..  +.|++|.
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~   90 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAF   90 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEE
Confidence            455778999999999999999999999999999999986      56899999999999999999999875  7899999


Q ss_pred             EEEecCCC
Q 005812          290 VDWAVPKN  297 (676)
Q Consensus       290 v~~a~~~~  297 (676)
                      |.|++++.
T Consensus        91 V~~S~~k~   98 (100)
T 3r27_A           91 VNYSTSQK   98 (100)
T ss_dssp             EEECSCSC
T ss_pred             EEeccccc
Confidence            99998764

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

Probab=99.63  E-value=6.3e-16  Score=123.78  Aligned_cols=75  Identities=15%  Similarity=0.179  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      .....|||+||++.+|+++|+++|.+||+|.++.+..      ++|||||+|.++++|.+|++.||+..+.|+.|+|.++
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            4567899999999999999999999999999999976      6899999999999999999999999999999999998


Q ss_pred             c
Q 005812          294 V  294 (676)
Q Consensus       294 ~  294 (676)
                      .
T Consensus        79 ~   79 (89)
T 2wbr_A           79 S   79 (89)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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

Probab=99.63  E-value=5.6e-16  Score=132.98  Aligned_cols=85  Identities=27%  Similarity=0.359  Sum_probs=79.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee---c
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL---K  498 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l---~  498 (676)
                      ..+.++|||+|||+.+++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|.+|+..||     +..+   .
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~~~~   84 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALH-----EQKTLPGM   84 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHT-----TTCCCTTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhc-----CCcccCCC
Confidence            3456899999999999999999999999999999999998889999999999999999999999999     8887   8


Q ss_pred             CcEEEEEEccCch
Q 005812          499 GRQLTVLKALDKK  511 (676)
Q Consensus       499 gr~l~v~~a~~k~  511 (676)
                      |++|.|.++.++.
T Consensus        85 g~~l~v~~a~~~~   97 (106)
T 2dgp_A           85 NRPIQVKPADSES   97 (106)
T ss_dssp             SSCCEEEECCCCS
T ss_pred             CceEEEEECCccc
Confidence            9999999998754

>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

Probab=99.63  E-value=1.5e-15  Score=125.08  Aligned_cols=81  Identities=22%  Similarity=0.409  Sum_probs=76.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|++ +++..+.|+.|.|.
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            45577899999999999999999999999999999999998899999999999999999999997 58899999999998


Q ss_pred             Ee
Q 005812          292 WA  293 (676)
Q Consensus       292 ~a  293 (676)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.6e-15  Score=126.22  Aligned_cols=81  Identities=17%  Similarity=0.299  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      ...++|||+|||+.+++++|+++|+.| .|..|.|+.+ .++.++|||||+|.+.++|.+|+. ||     +..|+|+.|
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~-----g~~~~gr~i   79 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CN-----REYMGGRYI   79 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SC-----SEEETTEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hC-----CceeCCcEE
Confidence            345899999999999999999999999 9999999998 789999999999999999999999 99     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        80 ~v~~a~~~~   88 (91)
T 2dgw_A           80 EVFREKSGP   88 (91)
T ss_dssp             EEEEESSCC
T ss_pred             EEEECCcCC
Confidence            999998763

>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

Probab=99.63  E-value=6.4e-16  Score=130.53  Aligned_cols=82  Identities=20%  Similarity=0.263  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      ..++|||+|||+.+++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|.+|++.||     +..|+|+.|.
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~-----g~~~~g~~l~   88 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLN-----DRPIGSRKVK   88 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTT-----TCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhC-----CCeeCCeEEE
Confidence            35799999999999999999999999999988888888899999999999999999999999999     9999999999


Q ss_pred             EEEccCc
Q 005812          504 VLKALDK  510 (676)
Q Consensus       504 v~~a~~k  510 (676)
                      |.++..+
T Consensus        89 V~~a~~~   95 (98)
T 2cqp_A           89 LVLGSGP   95 (98)
T ss_dssp             EEESSCS
T ss_pred             EEEcCCC
Confidence            9998754

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

Probab=99.63  E-value=7.1e-16  Score=133.99  Aligned_cols=85  Identities=25%  Similarity=0.297  Sum_probs=79.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCcee--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCC
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVV--------SFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGL  493 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~--------~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~  493 (676)
                      ..+.++|||+|||+.+++++|+++|+.||.|.        .|+|+.++.++.++|||||+|.+.++|.+|+..||     
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~-----   86 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFD-----   86 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHT-----
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcC-----
Confidence            34568999999999999999999999999999        59999998899999999999999999999999999     


Q ss_pred             CeeecCcEEEEEEccCch
Q 005812          494 GIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       494 g~~l~gr~l~v~~a~~k~  511 (676)
                      +..|.|+.|.|.++.++.
T Consensus        87 g~~~~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           87 GKDFQGSKLKVSLARKKP  104 (113)
T ss_dssp             TCEETTEECEEECSSCCC
T ss_pred             CCccCCCEEEEEECCCCC
Confidence            999999999999998764

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

Probab=99.63  E-value=5.6e-16  Score=132.48  Aligned_cols=84  Identities=24%  Similarity=0.338  Sum_probs=78.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHh-CCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCee-ecC
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSA-FGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIF-LKG  499 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~-~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~-l~g  499 (676)
                      ..+.++|||+|||+.+++++|+++|+. ||.|..|.|+.+. ++.++|||||+|.+.++|.+|+..|+     +.. |+|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~~g   79 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQ-----GAVGLGS   79 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTT-----TCCSSSS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHcc-----CCcccCC
Confidence            345689999999999999999999999 9999999999997 89999999999999999999999999     999 999


Q ss_pred             cEEEEEEccCch
Q 005812          500 RQLTVLKALDKK  511 (676)
Q Consensus       500 r~l~v~~a~~k~  511 (676)
                      ++|.|.++.++.
T Consensus        80 ~~l~v~~a~~~~   91 (104)
T 2dhg_A           80 KPVRLSVAIPKA   91 (104)
T ss_dssp             SCCCCCBCCCCC
T ss_pred             EeEEEEEccCCC
Confidence            999999997764

>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

Probab=99.63  E-value=9.6e-16  Score=126.91  Aligned_cols=80  Identities=24%  Similarity=0.373  Sum_probs=76.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      .++|||+|||..+++++|+++|+.||.|.++.++.++.++.++|||||+|.+.++|.+|+ .|+|..+.|+.|.|.++.+
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            479999999999999999999999999999999999889999999999999999999999 8999999999999999876


Q ss_pred             C
Q 005812          296 K  296 (676)
Q Consensus       296 ~  296 (676)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

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

Probab=99.63  E-value=1.6e-15  Score=132.34  Aligned_cols=84  Identities=24%  Similarity=0.433  Sum_probs=78.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|++||.|..|+|+.++.++.++|||||+|.+.++|.+|+..++     + .|.|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~-----~-~~~g~   86 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-----P-IIDGR   86 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSS-----C-EETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCC-----C-cCCCE
Confidence            34456899999999999999999999999999999999998899999999999999999999999999     8 89999


Q ss_pred             EEEEEEccCc
Q 005812          501 QLTVLKALDK  510 (676)
Q Consensus       501 ~l~v~~a~~k  510 (676)
                      .|.|.++.++
T Consensus        87 ~l~V~~a~~~   96 (116)
T 2cqd_A           87 KANVNLAYLG   96 (116)
T ss_dssp             ECEEEESTTT
T ss_pred             EEEEEEcccC
Confidence            9999998764

>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

Probab=99.63  E-value=2.5e-15  Score=128.13  Aligned_cols=84  Identities=24%  Similarity=0.394  Sum_probs=77.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+.  +     +..|+|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~-----~~~~~g~   83 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--Q-----RHMIDGR   83 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--S-----CEEETTE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--c-----CCeeCCe
Confidence            34456899999999999999999999999999999999998889999999999999999999998  4     6799999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        84 ~l~v~~a~~~~   94 (103)
T 2cqg_A           84 WCDCKLPNSKQ   94 (103)
T ss_dssp             EEEEECCCTTC
T ss_pred             EEEEEecCCCC
Confidence            99999998764

>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

Probab=99.63  E-value=1.2e-15  Score=128.26  Aligned_cols=79  Identities=16%  Similarity=0.238  Sum_probs=74.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHH----HHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          424 LQNTIFICNLPFDLDNEEVK----QRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~----~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      .+++|||+|||+.+++++|+    ++|++||.|..|+|+.+..+   +|||||+|.+.++|.+|+..||     |..|+|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~-----g~~~~g   79 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLH-----RYKIGS   79 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHT-----TEEETT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhC-----CCEECC
Confidence            45799999999999999999    99999999999999988654   8899999999999999999999     999999


Q ss_pred             cEEEEEEccCc
Q 005812          500 RQLTVLKALDK  510 (676)
Q Consensus       500 r~l~v~~a~~k  510 (676)
                      ++|.|.+|.++
T Consensus        80 r~l~V~~a~~~   90 (96)
T 2dgx_A           80 KKILVSLATGA   90 (96)
T ss_dssp             EEEEEEECCCS
T ss_pred             eEEEEEEcCCC
Confidence            99999999765

>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

Probab=99.63  E-value=1e-15  Score=131.35  Aligned_cols=87  Identities=26%  Similarity=0.390  Sum_probs=81.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee---CCee
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF---GKRP  287 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~---~g~~  287 (676)
                      ......++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|++.||+..+   .|+.
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            3456678999999999999999999999999999999999998999999999999999999999999999988   8999


Q ss_pred             EEEEEecCCC
Q 005812          288 IAVDWAVPKN  297 (676)
Q Consensus       288 i~v~~a~~~~  297 (676)
                      |.|.|+.++.
T Consensus        88 l~v~~a~~~~   97 (106)
T 2dgp_A           88 IQVKPADSES   97 (106)
T ss_dssp             CEEEECCCCS
T ss_pred             EEEEECCccc
Confidence            9999997764

>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

Probab=99.63  E-value=1.5e-15  Score=129.75  Aligned_cols=85  Identities=24%  Similarity=0.428  Sum_probs=79.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCC-CCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDT-GLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~-~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      .....++|||+|||+.+++++|+++|+.|| |..|.|+.++.+ +.++|||||+|.+.++|++|+ .|++..|.|+.|.|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            345678999999999999999999999999 999999999887 899999999999999999999 89999999999999


Q ss_pred             EEecCCCC
Q 005812          291 DWAVPKNI  298 (676)
Q Consensus       291 ~~a~~~~~  298 (676)
                      .++.++..
T Consensus        89 ~~a~~~~~   96 (104)
T 1wi8_A           89 DVADQAQD   96 (104)
T ss_dssp             EECCCCCC
T ss_pred             EEccCCCC
Confidence            99987653

>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

Probab=99.63  E-value=7.3e-16  Score=136.84  Aligned_cols=87  Identities=26%  Similarity=0.423  Sum_probs=81.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      ......++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|++|+..|+|..|.|+.|.|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34566789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEecCCC
Q 005812          291 DWAVPKN  297 (676)
Q Consensus       291 ~~a~~~~  297 (676)
                      .|+.++.
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9997754

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

Probab=99.63  E-value=7.5e-16  Score=132.68  Aligned_cols=85  Identities=22%  Similarity=0.383  Sum_probs=76.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...++++|||+|||+.+++++|+++|+.||.|..|+++.+..+|.++|||||+|.+.++|.+|+..+      +..|+|+
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~------~~~l~g~   94 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS------RHELDSK   94 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS------CEEETTE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC------CCcCCCE
Confidence            3445689999999999999999999999999999999999888999999999999999999999875      5899999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        95 ~l~V~~a~~~~  105 (109)
T 2rs2_A           95 TIDPKVAFPRR  105 (109)
T ss_dssp             EEEEEECCCCC
T ss_pred             EEEEEEccCCC
Confidence            99999998764

>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

Probab=99.63  E-value=2.1e-15  Score=129.63  Aligned_cols=83  Identities=25%  Similarity=0.424  Sum_probs=78.5

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      ......++|||+|||+.+++++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|.+|++.|+|..|.|+.|.|
T Consensus        24 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V  102 (107)
T 3ulh_A           24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI  102 (107)
T ss_dssp             CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            345677999999999999999999999999999999999998 8999999999999999999999999999999999999


Q ss_pred             EEec
Q 005812          291 DWAV  294 (676)
Q Consensus       291 ~~a~  294 (676)
                      .++.
T Consensus       103 ~~a~  106 (107)
T 3ulh_A          103 QLVT  106 (107)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9985

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

Probab=99.63  E-value=1.7e-15  Score=131.55  Aligned_cols=87  Identities=22%  Similarity=0.348  Sum_probs=81.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceE--------EEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVW--------NVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF  283 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~--------~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  283 (676)
                      .....++|||+|||+.+++++|+++|+.||.|.        .|.|+.++.++.++|||||+|.+.++|.+|++.|||..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            455678999999999999999999999999999        699999988999999999999999999999999999999


Q ss_pred             CCeeEEEEEecCCCC
Q 005812          284 GKRPIAVDWAVPKNI  298 (676)
Q Consensus       284 ~g~~i~v~~a~~~~~  298 (676)
                      .|+.|+|.|+.++..
T Consensus        91 ~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           91 QGSKLKVSLARKKPP  105 (113)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCCEEEEEECCCCCC
Confidence            999999999987653

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

Probab=99.63  E-value=1.2e-15  Score=127.99  Aligned_cols=83  Identities=23%  Similarity=0.365  Sum_probs=77.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|++||.|.+|.|+.++. +.++|||||+|.+.++|.+|++.||+..|.|+.|.|.
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            445678999999999999999999999999999999999875 8899999999999999999999999999999999999


Q ss_pred             EecC
Q 005812          292 WAVP  295 (676)
Q Consensus       292 ~a~~  295 (676)
                      |+..
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9853

>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}

Probab=99.62  E-value=2e-15  Score=131.46  Aligned_cols=85  Identities=26%  Similarity=0.403  Sum_probs=79.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||.++++++|+++|+.||.|..|.|+.+. +|.++|||||+|.+.++|++|++.|+|..|.|+.|.|.|
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999987 899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 005812          293 AVPKNI  298 (676)
Q Consensus       293 a~~~~~  298 (676)
                      +.+...
T Consensus        83 a~~~~~   88 (116)
T 2fy1_A           83 AKKPSF   88 (116)
T ss_dssp             CCCSSC
T ss_pred             CCCCCC
Confidence            987653

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

Probab=99.62  E-value=6.6e-16  Score=131.14  Aligned_cols=81  Identities=21%  Similarity=0.351  Sum_probs=76.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|++++. |.++|||||+|.+.++|.+|+. +++..|.|+.|.|.|
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   85 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            44568999999999999999999999999999999999986 9999999999999999999999 899999999999998


Q ss_pred             ecC
Q 005812          293 AVP  295 (676)
Q Consensus       293 a~~  295 (676)
                      +..
T Consensus        86 ~~~   88 (103)
T 1s79_A           86 KDD   88 (103)
T ss_dssp             HHH
T ss_pred             chH
Confidence            754

>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

Probab=99.62  E-value=4.5e-16  Score=130.65  Aligned_cols=80  Identities=20%  Similarity=0.282  Sum_probs=75.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+|++.||     +..|+|++|.|
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~-----g~~~~gr~l~v   89 (95)
T 2ek1_A           15 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLN-----DRPIGSRKVKL   89 (95)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHT-----TCEETTEECEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhC-----CCeECCcEEEE
Confidence            4799999999999999999999999999998899988899999999999999999999999999     99999999999


Q ss_pred             EEccC
Q 005812          505 LKALD  509 (676)
Q Consensus       505 ~~a~~  509 (676)
                      .++.+
T Consensus        90 ~~a~s   94 (95)
T 2ek1_A           90 SGPSS   94 (95)
T ss_dssp             ECCC-
T ss_pred             EeccC
Confidence            98753

>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

Probab=99.62  E-value=6.4e-16  Score=134.74  Aligned_cols=81  Identities=23%  Similarity=0.397  Sum_probs=74.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..++++|||+|||+.+++++|+++|+.||.|..|.++.+   +.++|||||+|.+.++|.+|+..||     |..|+|+.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~   76 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLS-----GFNVSNRY   76 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHT-----TCBSSSCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcC-----CCEECCeE
Confidence            345689999999999999999999999999999998865   4569999999999999999999999     99999999


Q ss_pred             EEEEEccCc
Q 005812          502 LTVLKALDK  510 (676)
Q Consensus       502 l~v~~a~~k  510 (676)
                      |.|.++.++
T Consensus        77 l~v~~a~~~   85 (115)
T 3lqv_A           77 LVVLYYNAN   85 (115)
T ss_dssp             CEEEECCHH
T ss_pred             EEEEEecCC
Confidence            999998754

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

Probab=99.62  E-value=1.2e-15  Score=133.58  Aligned_cols=83  Identities=27%  Similarity=0.409  Sum_probs=78.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+++++++|+++|++||.|.+|.|+.++.++.++|||||+|.+.++|++|++.|||..|.|+.|+|.
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             Eec
Q 005812          292 WAV  294 (676)
Q Consensus       292 ~a~  294 (676)
                      |++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            873

>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

Probab=99.62  E-value=1.9e-15  Score=127.01  Aligned_cols=83  Identities=24%  Similarity=0.303  Sum_probs=76.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH----HhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCee
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIK----DMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRP  287 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~----~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  287 (676)
                      .....++|||+|||+.+++++|+    ++|++||.|.+|.|+.++.+   +|||||+|.+.++|++|++.|||..|.|+.
T Consensus         5 ~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~   81 (96)
T 2dgx_A            5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKK   81 (96)
T ss_dssp             CCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            34567899999999999999999    99999999999999988654   789999999999999999999999999999


Q ss_pred             EEEEEecCCC
Q 005812          288 IAVDWAVPKN  297 (676)
Q Consensus       288 i~v~~a~~~~  297 (676)
                      |+|.++.+..
T Consensus        82 l~V~~a~~~~   91 (96)
T 2dgx_A           82 ILVSLATGAS   91 (96)
T ss_dssp             EEEEECCCSS
T ss_pred             EEEEEcCCCC
Confidence            9999997754

>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

Probab=99.62  E-value=4.6e-15  Score=126.49  Aligned_cols=86  Identities=34%  Similarity=0.517  Sum_probs=78.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      ......++|||+|||+.+++++|+++|+.||.|..|.|+.+..  .++|||||+|.+.++|.+|+..|++..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3456679999999999999999999999999999999998753  38999999999999999999999999999999999


Q ss_pred             EEecCCCC
Q 005812          291 DWAVPKNI  298 (676)
Q Consensus       291 ~~a~~~~~  298 (676)
                      .|+.++..
T Consensus        88 ~~a~~~~~   95 (103)
T 2cq3_A           88 NNATARVM   95 (103)
T ss_dssp             EECCSSCC
T ss_pred             EEcccCCC
Confidence            99987653

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

Probab=99.62  E-value=1.3e-15  Score=126.91  Aligned_cols=82  Identities=29%  Similarity=0.456  Sum_probs=76.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.+  ++.++|||||+|.+.++|.+|+..||     +..|+|+.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~-----g~~~~g~~l   78 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMN-----GMKLSGREI   78 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHT-----TCCBTTBCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhC-----CCEECCcEE
Confidence            34689999999999999999999999999999998874  68899999999999999999999999     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        79 ~v~~a~~~~   87 (92)
T 2dgv_A           79 DVRIDRNAS   87 (92)
T ss_dssp             CCEECSCCS
T ss_pred             EEEEcCCCC
Confidence            999988754

>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

Probab=99.62  E-value=1.1e-15  Score=129.05  Aligned_cols=85  Identities=21%  Similarity=0.373  Sum_probs=78.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|++|++.|||..|.|+.|+|.
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34556899999999999999999999999999988888888899999999999999999999999999999999999999


Q ss_pred             EecCC
Q 005812          292 WAVPK  296 (676)
Q Consensus       292 ~a~~~  296 (676)
                      ++..+
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98654

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

Probab=99.62  E-value=1.8e-15  Score=126.06  Aligned_cols=84  Identities=31%  Similarity=0.429  Sum_probs=78.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||.++++++|+++|++||.|..|.|+.+  ++.++|||||+|.+.++|.+|++.|++..+.|+.|.|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   81 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVR   81 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            4456789999999999999999999999999999999874  78899999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.+..
T Consensus        82 ~a~~~~   87 (92)
T 2dgv_A           82 IDRNAS   87 (92)
T ss_dssp             ECSCCS
T ss_pred             EcCCCC
Confidence            997764

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

Probab=99.62  E-value=1.1e-15  Score=133.40  Aligned_cols=83  Identities=24%  Similarity=0.492  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      ...++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+.. +     +..|+|+.|
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~-----~~~~~g~~l   98 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-R-----PHSIDGRVV   98 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-C-----SEEETTEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-C-----CcEECCEEE
Confidence            3458999999999999999999999999999999999988899999999999999999999988 8     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        99 ~V~~a~~~~  107 (116)
T 1x4b_A           99 EPKRAVARE  107 (116)
T ss_dssp             EEECCSSCC
T ss_pred             EEEECCCCc
Confidence            999998874

>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

Probab=99.62  E-value=2.3e-15  Score=130.24  Aligned_cols=91  Identities=35%  Similarity=0.504  Sum_probs=80.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCC-CCCCeeecC
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTT-SGLGIFLKG  499 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~-~~~g~~l~g  499 (676)
                      ...+.++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+..||.. ...+..|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            4445789999999999999999999999999999999999889999999999999999999999998610 011588999


Q ss_pred             cEEEEEEccCch
Q 005812          500 RQLTVLKALDKK  511 (676)
Q Consensus       500 r~l~v~~a~~k~  511 (676)
                      +.|.|.++.++.
T Consensus        91 ~~l~v~~a~~~~  102 (111)
T 1x4h_A           91 RQLKVDLAVTRD  102 (111)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEEECCCCc
Confidence            999999998764

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=2.1e-15  Score=127.24  Aligned_cols=81  Identities=22%  Similarity=0.263  Sum_probs=71.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..++++|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|+..|+..   +..|.|++
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~---~~~~~Gr~   82 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAV---TPHLRNQP   82 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHS---CCEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccC---CceECCcE
Confidence            345789999999999999999999999999999987643      799999999999999999987411   68899999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.|+.++.
T Consensus        83 l~V~~a~~~~   92 (101)
T 2cq1_A           83 IYIQYSNHKE   92 (101)
T ss_dssp             CEEEECSCSS
T ss_pred             EEEEEcCccc
Confidence            9999998754

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

Probab=99.62  E-value=1.7e-15  Score=129.43  Aligned_cols=86  Identities=23%  Similarity=0.425  Sum_probs=80.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhcc-CCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCce-eCCeeEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSP-VGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK-FGKRPIA  289 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~-~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~-~~g~~i~  289 (676)
                      .....++|||+|||+++++++|+++|+. ||.|.+|.|+.++ ++.++|||||+|.+.++|.+|++.|++.. |.|+.|.
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            3456789999999999999999999999 9999999999998 89999999999999999999999999999 9999999


Q ss_pred             EEEecCCCC
Q 005812          290 VDWAVPKNI  298 (676)
Q Consensus       290 v~~a~~~~~  298 (676)
                      |.++.++..
T Consensus        84 v~~a~~~~~   92 (104)
T 2dhg_A           84 LSVAIPKAS   92 (104)
T ss_dssp             CCBCCCCCS
T ss_pred             EEEccCCCc
Confidence            999977653

>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

Probab=99.62  E-value=6.4e-16  Score=136.58  Aligned_cols=87  Identities=20%  Similarity=0.336  Sum_probs=79.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ....++|||+|||+.+++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|.+||. ||     +..|+|+.
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~-----g~~~~gr~   95 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RH-----KQYMGNRF   95 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SC-----SBCSTTSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hC-----CCeECCcE
Confidence            3456899999999999999999999999999986677777889999999999999999999999 99     99999999


Q ss_pred             EEEEEccCchhhh
Q 005812          502 LTVLKALDKKLAH  514 (676)
Q Consensus       502 l~v~~a~~k~~~~  514 (676)
                      |.|.++.+++...
T Consensus        96 i~V~~a~~~~~~~  108 (124)
T 1wel_A           96 IQVHPITKKGMLE  108 (124)
T ss_dssp             BEEEEECHHHHHH
T ss_pred             EEEEECCHHHHHH
Confidence            9999998776443

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=9e-16  Score=129.23  Aligned_cols=82  Identities=21%  Similarity=0.388  Sum_probs=73.9

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCC--ceeCCeeE
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG--QKFGKRPI  288 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~--~~~~g~~i  288 (676)
                      ......++|||+|||+++++++|+++|++||.|.+|.|+++      +|||||+|.+.++|..|++.|++  ..|.|++|
T Consensus        11 ~~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l   84 (105)
T 1sjq_A           11 GSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPI   84 (105)
T ss_dssp             -CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            35667889999999999999999999999999999999874      69999999999999999998864  78999999


Q ss_pred             EEEEecCCCC
Q 005812          289 AVDWAVPKNI  298 (676)
Q Consensus       289 ~v~~a~~~~~  298 (676)
                      +|.|+.++..
T Consensus        85 ~V~~A~~~~~   94 (105)
T 1sjq_A           85 YIQFSNHKEL   94 (105)
T ss_dssp             CBCCCSSSSC
T ss_pred             EEEEcCCCCC
Confidence            9999987654

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

Probab=99.62  E-value=3.2e-16  Score=139.96  Aligned_cols=83  Identities=16%  Similarity=0.271  Sum_probs=78.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE--EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCe----
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS--FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGI----  495 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~--v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~----  495 (676)
                      ....++|||+|||+.+++++|+++|++||.|..  |+|++++.++.++|||||+|.+. +|.+|+..||     +.    
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~-----g~~~~~   93 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQ-----ALHPPL   93 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHT-----TCCCSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhc-----CCCCCc
Confidence            345689999999999999999999999999977  99999998999999999999999 9999999999     98    


Q ss_pred             eecCcEEEEEEccCc
Q 005812          496 FLKGRQLTVLKALDK  510 (676)
Q Consensus       496 ~l~gr~l~v~~a~~k  510 (676)
                      .|+||.|.|.++.++
T Consensus        94 ~~~gr~l~V~~a~~~  108 (131)
T 2m2b_A           94 TIDGKTINVEFAKGS  108 (131)
T ss_dssp             CGGGCCCCCEECCCS
T ss_pred             cCCCEEEEEEECCCC
Confidence            999999999999875

>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

Probab=99.62  E-value=2.9e-15  Score=129.11  Aligned_cols=83  Identities=19%  Similarity=0.291  Sum_probs=75.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.+   +.++|||||+|.+.++|.+|++.||     +..|+|+
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~   89 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRD-----GYDYDGY   89 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHT-----TCEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcC-----CCEECCe
Confidence            3445689999999999999999999999999999988654   4579999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        90 ~l~V~~a~~~~  100 (109)
T 1x4a_A           90 RLRVEFPRSGR  100 (109)
T ss_dssp             ECEEECCCCCC
T ss_pred             EEEEEEcccCC
Confidence            99999988753

>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*

Probab=99.62  E-value=8.7e-16  Score=136.25  Aligned_cols=86  Identities=20%  Similarity=0.308  Sum_probs=80.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...++++|||+|||+.+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~   92 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN-----GQDLMGQ   92 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHT-----TCBSSSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhC-----CCeeCCe
Confidence            33456899999999999999999999999999999999998899999999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        93 ~l~v~~a~~~~  103 (126)
T 3ex7_B           93 PISVDWCFVRG  103 (126)
T ss_dssp             BCEEEESEESS
T ss_pred             EEEEEEecCCC
Confidence            99999997654

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

Probab=99.62  E-value=4.4e-16  Score=124.43  Aligned_cols=75  Identities=24%  Similarity=0.405  Sum_probs=71.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEE
Q 005812          427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLK  506 (676)
Q Consensus       427 ~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~  506 (676)
                      +|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++ |+     +..|+|++|.|.+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~-----~~~~~g~~l~v~~   74 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IH-----FHEINNKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SS-----CCCSSSCCCEEEC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CC-----CCEECCEEEEEEe
Confidence            48999999999999999999999999999999998889999999999999999999997 89     9999999999987


Q ss_pred             c
Q 005812          507 A  507 (676)
Q Consensus       507 a  507 (676)
                      |
T Consensus        75 A   75 (75)
T 2mss_A           75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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

Probab=99.61  E-value=9.8e-16  Score=130.95  Aligned_cols=83  Identities=31%  Similarity=0.568  Sum_probs=79.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++|||+|||..+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            45799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCC
Q 005812          295 PKN  297 (676)
Q Consensus       295 ~~~  297 (676)
                      ++.
T Consensus        87 ~~~   89 (104)
T 1p1t_A           87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             Ccc
Confidence            764

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

Probab=99.61  E-value=5.6e-16  Score=123.83  Aligned_cols=75  Identities=19%  Similarity=0.371  Sum_probs=72.2

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       218 ~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      +|||+|||+++++++|+++|++||.|.+|.++.++.++.++|||||+|.+.++|++|++ |++..+.|+.|.|.||
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            48999999999999999999999999999999998899999999999999999999998 8999999999999875

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

Probab=99.61  E-value=3e-15  Score=130.67  Aligned_cols=85  Identities=21%  Similarity=0.322  Sum_probs=79.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|++|++.|++ .|.|+.|.|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            455679999999999999999999999999999999999988999999999999999999999999998 8999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.+..
T Consensus        92 ~a~~~~   97 (116)
T 2cqd_A           92 LAYLGA   97 (116)
T ss_dssp             ESTTTC
T ss_pred             EcccCC
Confidence            997653

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

Probab=99.61  E-value=2.6e-16  Score=133.35  Aligned_cols=84  Identities=23%  Similarity=0.352  Sum_probs=75.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQ-VTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~-~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      .....++|||+|||+.+++++|+++|+.|| |..|+++.+. .+|.++|||||+|.+.++|.+|+ .|+     |..|+|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~-----g~~~~g   87 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLN-----EESLGN   87 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTT-----TCCBTT
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcC-----CCEECC
Confidence            344568999999999999999999999999 9999999887 58999999999999999999999 899     999999


Q ss_pred             cEEEEEEccCch
Q 005812          500 RQLTVLKALDKK  511 (676)
Q Consensus       500 r~l~v~~a~~k~  511 (676)
                      +.|.|.++.+++
T Consensus        88 ~~l~V~~a~~~~   99 (100)
T 2j76_E           88 RRIRVDVADQAQ   99 (100)
T ss_dssp             BCCCCEECCCSC
T ss_pred             eEEEEEeccCCC
Confidence            999999998753

>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

Probab=99.61  E-value=1.4e-15  Score=132.14  Aligned_cols=84  Identities=17%  Similarity=0.208  Sum_probs=77.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCce-eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEV-VSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v-~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      .+.++|||+|||+.+++++|+++|+.||.| ..|+|+.+. ++.++|||||+|.+.++|.+|+.. |     +..|+|+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~-----~~~~~gr~   85 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-H-----RKKLNGRE   85 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-C-----SEEETTEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-C-----CCccCCeE
Confidence            346899999999999999999999999999 889999997 899999999999999999999987 9     99999999


Q ss_pred             EEEEEccCchhh
Q 005812          502 LTVLKALDKKLA  513 (676)
Q Consensus       502 l~v~~a~~k~~~  513 (676)
                      |.|.++.++...
T Consensus        86 i~v~~a~~~~~~   97 (114)
T 2cpy_A           86 AFVHVVTLEDMR   97 (114)
T ss_dssp             EEEEEECHHHHH
T ss_pred             EEEEECCHHHHH
Confidence            999999876533

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

Probab=99.61  E-value=1.4e-15  Score=134.03  Aligned_cols=85  Identities=22%  Similarity=0.337  Sum_probs=75.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHH----HHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCee
Q 005812          421 EDELQNTIFICNLPFDLDNEEVK----QRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIF  496 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~----~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~  496 (676)
                      ...++++|||+|||+.+++++|+    ++|++||.|..|.+..   ++.++|||||+|.+.++|..|+..||     |..
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~ln-----g~~   96 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQ-----GYP   96 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHST-----TCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHC-----CCE
Confidence            44557899999999999999876    7999999999987643   57889999999999999999999999     999


Q ss_pred             ecCcEEEEEEccCchhh
Q 005812          497 LKGRQLTVLKALDKKLA  513 (676)
Q Consensus       497 l~gr~l~v~~a~~k~~~  513 (676)
                      |.|++|.|.||.++...
T Consensus        97 l~gr~l~V~~a~~~~~~  113 (127)
T 2a3j_A           97 FQGNPLVITFSETPQSQ  113 (127)
T ss_dssp             CTTSCCEEEECCCCCHH
T ss_pred             eCCCEEEEEEccCcchh
Confidence            99999999999887543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=4e-15  Score=123.73  Aligned_cols=83  Identities=23%  Similarity=0.380  Sum_probs=77.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+++++++|+++|+.| .|..|.|+.+ .+|+++|||||+|.+.++|.+|+. |||..|.|+.|.|.
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~   82 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVF   82 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEE
Confidence            44567899999999999999999999999 8999999998 689999999999999999999999 99999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      ++.++.
T Consensus        83 ~a~~~~   88 (91)
T 2dgw_A           83 REKSGP   88 (91)
T ss_dssp             EESSCC
T ss_pred             ECCcCC
Confidence            997753

>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

Probab=99.61  E-value=8.5e-16  Score=128.97  Aligned_cols=83  Identities=22%  Similarity=0.392  Sum_probs=75.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.||+..|.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            34568999999999999999999999999999898988888999999999999999999999999999999999999998


Q ss_pred             ecC
Q 005812          293 AVP  295 (676)
Q Consensus       293 a~~  295 (676)
                      +.+
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            753

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

Probab=99.61  E-value=1.5e-15  Score=139.31  Aligned_cols=83  Identities=16%  Similarity=0.268  Sum_probs=78.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCC--ceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVG--LVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G--~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ..++|||+|||+++++++|+++|+.||  .|.+|.|+.++.+|+++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            457999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 005812          293 AVPKN  297 (676)
Q Consensus       293 a~~~~  297 (676)
                      +.++.
T Consensus       134 a~~~~  138 (156)
T 3n9u_C          134 ATRQN  138 (156)
T ss_dssp             CCHHH
T ss_pred             cCCCc
Confidence            97653

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

Probab=99.61  E-value=6.5e-16  Score=131.27  Aligned_cols=76  Identities=21%  Similarity=0.337  Sum_probs=71.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      ++|||+|||+.+++++|+++|++||.|..|.++.+     ++|||||+|.+.++|.+|+..|+     +..++|+.|.|.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l~V~   70 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLD-----GKVICGSRVRVE   70 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHH-----HSCSSSCCCEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHC-----CCeECCcEEEEE
Confidence            47999999999999999999999999999998866     68999999999999999999999     999999999999


Q ss_pred             EccCch
Q 005812          506 KALDKK  511 (676)
Q Consensus       506 ~a~~k~  511 (676)
                      ++.++.
T Consensus        71 ~a~~~~   76 (101)
T 2hvz_A           71 LSTGMP   76 (101)
T ss_dssp             ESSSCC
T ss_pred             EccCCC
Confidence            998764

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

Probab=99.61  E-value=1.6e-15  Score=130.70  Aligned_cols=83  Identities=23%  Similarity=0.532  Sum_probs=76.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      .....++|||+|||..+++++|+++|++||.|..|.++.+.  +.++|||||+|.+.++|.+|+..||     |..|+|+
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~-----g~~~~g~   97 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLH-----GTVVEGR   97 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHT-----TCEETTE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcC-----CCEECCE
Confidence            44456899999999999999999999999999999998885  3489999999999999999999999     9999999


Q ss_pred             EEEEEEccCc
Q 005812          501 QLTVLKALDK  510 (676)
Q Consensus       501 ~l~v~~a~~k  510 (676)
                      .|.|.++.++
T Consensus        98 ~l~V~~a~~~  107 (109)
T 2err_A           98 KIEVNNATAR  107 (109)
T ss_dssp             ECEEEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999998875

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.61  E-value=2.2e-15  Score=131.64  Aligned_cols=82  Identities=16%  Similarity=0.218  Sum_probs=76.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCc---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGE---VVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~---v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      ...++|||+|||+++++++|+++|+.||.   |..|+|+.+.. ++++|||||+|.+.++|.+|++ +|     +..|+|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~-----g~~~~g   87 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KD-----RESMGH   87 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GT-----TEEETT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cC-----CCeECC
Confidence            34689999999999999999999999999   89999999876 9999999999999999999998 99     999999


Q ss_pred             cEEEEEEccCch
Q 005812          500 RQLTVLKALDKK  511 (676)
Q Consensus       500 r~l~v~~a~~k~  511 (676)
                      |.|.|.++..++
T Consensus        88 r~i~V~~a~~~~   99 (118)
T 2db1_A           88 RYIEVFKSHRTE   99 (118)
T ss_dssp             EEEEEEEECHHH
T ss_pred             eEEEEEECCHHH
Confidence            999999987554

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

Probab=99.61  E-value=2.4e-16  Score=129.36  Aligned_cols=80  Identities=23%  Similarity=0.321  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      ++++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|+..||     |..|.|+.|+
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~~~   78 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALK-----ASGVQAQMAK   78 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHH-----HHTCCEESCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhc-----CCeEeeEEEe
Confidence            45899999999999999999999999999999999998899999999999999999999999999     9999999998


Q ss_pred             EEEcc
Q 005812          504 VLKAL  508 (676)
Q Consensus       504 v~~a~  508 (676)
                      +.++.
T Consensus        79 ~~~~~   83 (85)
T 1x4e_A           79 QSGPS   83 (85)
T ss_dssp             SSCCC
T ss_pred             ecCCC
Confidence            87654

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.61  E-value=1.2e-15  Score=136.04  Aligned_cols=82  Identities=15%  Similarity=0.193  Sum_probs=76.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCc---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGE---VVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~---v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      ...++|||+|||+++|+++|+++|+.||.   |..|+|+.++. |+++|||||+|.+.++|.+|++ ||     +..|+|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~-----g~~l~g  114 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KD-----RESMGH  114 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TT-----EEESSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cC-----CCEECC
Confidence            34689999999999999999999999999   88999999976 9999999999999999999999 99     999999


Q ss_pred             cEEEEEEccCch
Q 005812          500 RQLTVLKALDKK  511 (676)
Q Consensus       500 r~l~v~~a~~k~  511 (676)
                      |.|.|.++.+++
T Consensus       115 r~i~V~~a~~~e  126 (136)
T 2hgl_A          115 RYIEVFKSHRTE  126 (136)
T ss_dssp             SEEEEEECCHHH
T ss_pred             EEEEEEECChHH
Confidence            999999987654

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

Probab=99.61  E-value=5.1e-15  Score=130.83  Aligned_cols=84  Identities=21%  Similarity=0.377  Sum_probs=78.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...++++|||+|||+.+++++|+++|+.||.|..|.|+.+. ++.++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~-----g~~~~g~  104 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYK-----GVPLDGR  104 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHT-----TEESSSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcC-----CCEECCc
Confidence            34557899999999999999999999999999999999987 89999999999999999999999999     9999999


Q ss_pred             EEEEEEccCc
Q 005812          501 QLTVLKALDK  510 (676)
Q Consensus       501 ~l~v~~a~~k  510 (676)
                      .|.|.+|.+.
T Consensus       105 ~l~V~~a~~~  114 (124)
T 2kt5_A          105 PMDIQLVASQ  114 (124)
T ss_dssp             EEEEEEECCT
T ss_pred             EEEEEEeCCC
Confidence            9999998765

>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*

Probab=99.61  E-value=1.9e-15  Score=134.06  Aligned_cols=87  Identities=26%  Similarity=0.556  Sum_probs=81.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            45567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus        98 ~a~~~~~  104 (126)
T 3ex7_B           98 WCFVRGP  104 (126)
T ss_dssp             ESEESSS
T ss_pred             EecCCCC
Confidence            9977643

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

Probab=99.61  E-value=5.4e-15  Score=126.05  Aligned_cols=84  Identities=24%  Similarity=0.396  Sum_probs=77.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|+.||.|..|.|+.++.+  ++|||||+|.+.++|.+|+..|++..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            4456789999999999999999999999999999999998533  68999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.++.
T Consensus        89 ~a~~~~   94 (103)
T 2cqi_A           89 WATTPS   94 (103)
T ss_dssp             ECCCTT
T ss_pred             ECCCCc
Confidence            998754

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

Probab=99.61  E-value=5.8e-16  Score=127.02  Aligned_cols=81  Identities=16%  Similarity=0.226  Sum_probs=76.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      .+.++|||+|||+++++++|+++|+.||.|..|.++.++.++.++|||||+|.+.++|.+|++.|||..+.|+.|++.|+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999988765


Q ss_pred             c
Q 005812          294 V  294 (676)
Q Consensus       294 ~  294 (676)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=1.7e-15  Score=129.62  Aligned_cols=86  Identities=21%  Similarity=0.349  Sum_probs=80.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|++|+.. ++..|.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            455678999999999999999999999999999999999988999999999999999999999998 9999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      ++.++..
T Consensus        91 ~a~~~~~   97 (105)
T 2dh8_A           91 PCTPRGM   97 (105)
T ss_dssp             CSCCSSC
T ss_pred             EccCCCC
Confidence            9987654

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

Probab=99.60  E-value=9.9e-16  Score=130.13  Aligned_cols=76  Identities=30%  Similarity=0.460  Sum_probs=71.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      ++|||+|||.++++++|+++|++||.|..|.++.+     ++|||||+|.+.++|.+|++.|+|..+.|+.|.|.|+.++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            47999999999999999999999999999999986     7899999999999999999999999999999999999775


Q ss_pred             C
Q 005812          297 N  297 (676)
Q Consensus       297 ~  297 (676)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.60  E-value=8.6e-16  Score=130.16  Aligned_cols=84  Identities=25%  Similarity=0.461  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccC-CCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNT-DTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      .....++|||+|||.++++++|+++|+.|| |.+|.|+.++ .+|+++|||||+|.+.++|.+|+ .|+|..|.|+.|.|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            345678999999999999999999999999 9999999988 58999999999999999999999 79999999999999


Q ss_pred             EEecCCC
Q 005812          291 DWAVPKN  297 (676)
Q Consensus       291 ~~a~~~~  297 (676)
                      .++.+++
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9997753

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

Probab=99.60  E-value=9.6e-15  Score=127.00  Aligned_cols=85  Identities=27%  Similarity=0.376  Sum_probs=78.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|+.||.|..|.|+.++ ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            34557899999999999999999999999999999999987 68899999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.+..
T Consensus        90 ~a~~~~   95 (114)
T 2do0_A           90 MDERAL   95 (114)
T ss_dssp             ECSCCC
T ss_pred             EcccCC
Confidence            986543

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

Probab=99.60  E-value=3.6e-15  Score=129.69  Aligned_cols=82  Identities=26%  Similarity=0.361  Sum_probs=76.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .++++|||+|||+.+++++|+++|+.||.|..|.|+.+. ++.++|||||+|.+.++|.+|+..||     +..|+|+.|
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l   86 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFN-----GQLLFDRPM   86 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHT-----TCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhC-----CCEeCCCEE
Confidence            346899999999999999999999999999999999986 58899999999999999999999999     999999999


Q ss_pred             EEEEccCc
Q 005812          503 TVLKALDK  510 (676)
Q Consensus       503 ~v~~a~~k  510 (676)
                      .|.++...
T Consensus        87 ~v~~a~~~   94 (114)
T 2do0_A           87 HVKMDERA   94 (114)
T ss_dssp             EEEECSCC
T ss_pred             EEEEcccC
Confidence            99998753

>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

Probab=99.60  E-value=7.1e-16  Score=129.90  Aligned_cols=80  Identities=21%  Similarity=0.235  Sum_probs=70.7

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          423 ELQNTIFICNLPF-DLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       423 ~~~~~l~V~nLp~-~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      .++++|||+|||+ .+++++|+++|++||.|.+|+|+++      +|||||+|.+.++|..|+..|+..   +..|.||+
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~---~~~~~Gr~   83 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTT---PALVFGKP   83 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHS---CCEETTEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCC---CceECCcE
Confidence            3578999999999 9999999999999999999988754      589999999999999999998811   35699999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.+|..+.
T Consensus        84 l~V~~a~~~~   93 (102)
T 1x4d_A           84 VRVHLSQKYK   93 (102)
T ss_dssp             CEEEEECCCT
T ss_pred             EEEEECCCCC
Confidence            9999998653

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

Probab=99.60  E-value=4.8e-15  Score=133.86  Aligned_cols=86  Identities=24%  Similarity=0.383  Sum_probs=81.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||.++++++|+++|+.||.|.+|.|+.++.+++++|||||+|.+.++|.+|++.|||..|.|+.|.|.|
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            44568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 005812          293 AVPKNI  298 (676)
Q Consensus       293 a~~~~~  298 (676)
                      +.++..
T Consensus       119 a~~~~~  124 (139)
T 1u6f_A          119 AASGHQ  124 (139)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987654

>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

Probab=99.60  E-value=4.7e-15  Score=128.98  Aligned_cols=84  Identities=21%  Similarity=0.440  Sum_probs=77.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee---
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL---  497 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l---  497 (676)
                      .....++|||+|||+.+++++|+++|+.||.|..|+|+.+. ++.++|||||+|.+.++|.+|+..||     |..|   
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~~~   94 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFN-----GKFIKTP   94 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHB-----TCCCCCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhC-----CCEEcCC
Confidence            33456899999999999999999999999999999999997 89999999999999999999999999     8888   


Q ss_pred             -----cCcEEEEEEccCc
Q 005812          498 -----KGRQLTVLKALDK  510 (676)
Q Consensus       498 -----~gr~l~v~~a~~k  510 (676)
                           .+++|.|.|+.++
T Consensus        95 ~~~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           95 PGVSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             TTSCCCSSCBEEEECCCS
T ss_pred             ccccCCCCceeEEccCCC
Confidence                 6888999998764

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.3e-15  Score=131.62  Aligned_cols=81  Identities=25%  Similarity=0.324  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..++++|||+|||+++++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|.+|++.|+..   +..|.|++
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~---~~~l~Gr~   98 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSV---TPVLRGQP   98 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHH---CCCBTTBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccC---CceECCeE
Confidence            445789999999999999999999999999999998865      799999999999999999988711   36899999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.+|.++.
T Consensus        99 l~V~~a~~k~  108 (119)
T 2ad9_A           99 IYIQFSNHKE  108 (119)
T ss_dssp             CEEEECSSSS
T ss_pred             EEEEEccCCC
Confidence            9999998764

>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

Probab=99.60  E-value=3.9e-15  Score=137.28  Aligned_cols=85  Identities=21%  Similarity=0.265  Sum_probs=80.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|.+|+..||     +..|+|+.
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~-----g~~~~g~~  110 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYIN-----GTRLDDRI  110 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTT-----TSEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhC-----CCEECCeE
Confidence            3456899999999999999999999999999999999998889999999999999999999999999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.|+.++.
T Consensus       111 l~V~~a~~~~  120 (156)
T 1h2v_Z          111 IRTDWDAGFK  120 (156)
T ss_dssp             CEEEEESCCC
T ss_pred             EEEEECCCCC
Confidence            9999998754

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

Probab=99.60  E-value=2.7e-15  Score=129.70  Aligned_cols=86  Identities=21%  Similarity=0.230  Sum_probs=78.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH---HhhccCCceEEEEEcccCCCC---CceeEEEEEecCHHHHHHHHHHhCCceeCC
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIK---DMFSPVGLVWNVYIPHNTDTG---LSKGFAFVKFTCKRDAESAIQKFNGQKFGK  285 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~---~~F~~~G~i~~v~i~~~~~~~---~~~g~afV~f~~~~~A~~A~~~l~~~~~~g  285 (676)
                      .....++|||+|||+++++++|+   ++|++||.|..|.|+.+..++   .++|||||+|.+.++|++|++.|||..|.|
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            34567899999999999999999   999999999999999887643   566999999999999999999999999999


Q ss_pred             eeEEEEEecCCC
Q 005812          286 RPIAVDWAVPKN  297 (676)
Q Consensus       286 ~~i~v~~a~~~~  297 (676)
                      +.|.|.|+.++.
T Consensus        91 r~l~V~~a~~k~  102 (111)
T 2cpi_A           91 RTLKASLGTTKY  102 (111)
T ss_dssp             EEEEEESCCCCS
T ss_pred             EEEEEEeccccc
Confidence            999999998775

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

Probab=99.60  E-value=2.5e-15  Score=129.95  Aligned_cols=83  Identities=22%  Similarity=0.356  Sum_probs=76.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHH---HHHHhCCceeEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee
Q 005812          424 LQNTIFICNLPFDLDNEEVK---QRFSAFGEVVSFVPVLHQVTK---RPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL  497 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~---~~F~~~G~v~~v~i~~~~~~~---~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l  497 (676)
                      ..++|||+|||+.+++++|+   ++|++||.|..|.|+.+..++   .++|||||+|.+.++|.+|++.||     +..|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~ln-----g~~~   88 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVN-----NVVV   88 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHT-----TEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhC-----CCEE
Confidence            45799999999999999999   999999999999998887543   566999999999999999999999     9999


Q ss_pred             cCcEEEEEEccCch
Q 005812          498 KGRQLTVLKALDKK  511 (676)
Q Consensus       498 ~gr~l~v~~a~~k~  511 (676)
                      +|++|.|.+|.++.
T Consensus        89 ~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           89 DGRTLKASLGTTKY  102 (111)
T ss_dssp             TTEEEEEESCCCCS
T ss_pred             CCEEEEEEeccccc
Confidence            99999999998764

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

Probab=99.60  E-value=5.3e-15  Score=133.77  Aligned_cols=82  Identities=23%  Similarity=0.392  Sum_probs=76.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...+.++|||+|||+.+++++|+++|++||.|..++++.++.++.++|||||+|.+.++|.+|++.||     +..|+|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~  133 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN-----ESELFGR  133 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHST-----EEEETTE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhC-----CCEECCE
Confidence            34456899999999999999999999999999999999998899999999999999999999999999     9999999


Q ss_pred             EEEEEEc
Q 005812          501 QLTVLKA  507 (676)
Q Consensus       501 ~l~v~~a  507 (676)
                      .|.|.+|
T Consensus       134 ~l~v~~A  140 (140)
T 2ku7_A          134 TIRVNLA  140 (140)
T ss_dssp             EEEEEC-
T ss_pred             EEEEEeC
Confidence            9999885

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

Probab=99.60  E-value=2e-15  Score=129.27  Aligned_cols=78  Identities=19%  Similarity=0.345  Sum_probs=72.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+++++++|+++|+.| .|..|.|+.+.. |+++|||||+|.+.++|.+|+ .+|     +..|+||.|.|
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~-----~~~~~gr~i~V   87 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRN-----RMLMIQRYVEV   87 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTT-----TEEETTEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcC-----CCeECCeEEEE
Confidence            4799999999999999999999999 899999999865 999999999999999999999 789     99999999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      ..+..+
T Consensus        88 ~~a~~~   93 (109)
T 2dnn_A           88 SPATER   93 (109)
T ss_dssp             EECCHH
T ss_pred             EECCcc
Confidence            988654

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

Probab=99.60  E-value=3.3e-15  Score=128.65  Aligned_cols=85  Identities=18%  Similarity=0.359  Sum_probs=76.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|+.||.|.+|.|+.++.+|.++|||||+|.+.++|.+|+..+ +..|.|+.|.|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            3456789999999999999999999999999999999999888999999999999999999999975 699999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      ++.++.
T Consensus       100 ~a~~~~  105 (109)
T 2rs2_A          100 VAFPRR  105 (109)
T ss_dssp             ECCCCC
T ss_pred             EccCCC
Confidence            998764

>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*

Probab=99.60  E-value=6.5e-16  Score=165.79  Aligned_cols=85  Identities=19%  Similarity=0.397  Sum_probs=80.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ...++|||+|||+.+|+++|..+|+.||.|..|.|+.+..++.++|||||+|.+.++|.+||..|||..|.|+.|.|.|+
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            44689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 005812          294 VPKNI  298 (676)
Q Consensus       294 ~~~~~  298 (676)
                      .+...
T Consensus       180 ~~~~~  184 (437)
T 3pgw_S          180 RGRTV  184 (437)
T ss_pred             CCCCC
Confidence            87644

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.4e-15  Score=128.99  Aligned_cols=80  Identities=18%  Similarity=0.247  Sum_probs=73.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      ...++|||+|||+++++++|+++|+.||.+ .|+|++++ +++++|||||+|.+.++|.+|+ .+|     +..|+||.|
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~-----~~~~~gr~i   84 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKD-----KANMQHRYV   84 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTS-----SCCSSSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHH-HhC-----CCeECCcEE
Confidence            345899999999999999999999999954 99999997 8999999999999999999999 579     999999999


Q ss_pred             EEEEccCc
Q 005812          503 TVLKALDK  510 (676)
Q Consensus       503 ~v~~a~~k  510 (676)
                      .|.++.+.
T Consensus        85 ~V~~~~~~   92 (102)
T 1wez_A           85 ELFLNSTA   92 (102)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCC
Confidence            99997764

>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

Probab=99.60  E-value=1.3e-15  Score=131.33  Aligned_cols=84  Identities=23%  Similarity=0.247  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCc-eeEEEEe-ecCCCCCcceEEEEEeCCHHHHHHHHHHc-CCCCCCC-eeecC
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGE-VVSFVPV-LHQVTKRPKGTGFLKFKTVEAATAAVSAS-KTTSGLG-IFLKG  499 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~-v~~v~i~-~~~~~~~~~g~afV~F~t~~~A~~Al~~l-~~~~~~g-~~l~g  499 (676)
                      +.++|||+|||+.+++++|+++|+.||. |..|.++ .+..++.++|||||+|.+.++|.+|+..| +     | ..|+|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~-----g~~~~~g   81 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMP-----GRIQLWG   81 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTT-----CCSCBTT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhC-----CCceecC
Confidence            4589999999999999999999999998 9999888 77778899999999999999999999999 5     5 89999


Q ss_pred             cEEEEEEccCchh
Q 005812          500 RQLTVLKALDKKL  512 (676)
Q Consensus       500 r~l~v~~a~~k~~  512 (676)
                      +.|.|.||.++..
T Consensus        82 ~~l~V~~a~~~~~   94 (109)
T 2dis_A           82 HQIAVDWAEPEID   94 (109)
T ss_dssp             BCCEEEESCSSCS
T ss_pred             CeEEEEEcCCCCC
Confidence            9999999988754

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

Probab=99.60  E-value=6.3e-15  Score=130.23  Aligned_cols=86  Identities=22%  Similarity=0.380  Sum_probs=80.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|.+|+..|+|..|.|+.|.|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            44567899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.+...
T Consensus       110 ~a~~~~~  116 (124)
T 2kt5_A          110 LVASQID  116 (124)
T ss_dssp             EECCTTC
T ss_pred             EeCCCCC
Confidence            9987654

>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

Probab=99.60  E-value=4.2e-15  Score=128.18  Aligned_cols=86  Identities=31%  Similarity=0.421  Sum_probs=79.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCc-eEEEEEc-ccCCCCCceeEEEEEecCHHHHHHHHHHhC--CceeCCeeE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGL-VWNVYIP-HNTDTGLSKGFAFVKFTCKRDAESAIQKFN--GQKFGKRPI  288 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~-i~~v~i~-~~~~~~~~~g~afV~f~~~~~A~~A~~~l~--~~~~~g~~i  288 (676)
                      ....++|||+|||+.+++++|+++|+.||. |.+|.++ .+..+|.++|||||+|.+.++|..|++.|+  +..+.|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            446789999999999999999999999998 9999998 788888999999999999999999999996  589999999


Q ss_pred             EEEEecCCCC
Q 005812          289 AVDWAVPKNI  298 (676)
Q Consensus       289 ~v~~a~~~~~  298 (676)
                      .|.|+.++..
T Consensus        85 ~V~~a~~~~~   94 (109)
T 2dis_A           85 AVDWAEPEID   94 (109)
T ss_dssp             EEEESCSSCS
T ss_pred             EEEEcCCCCC
Confidence            9999987654

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=1.2e-15  Score=133.10  Aligned_cols=86  Identities=23%  Similarity=0.306  Sum_probs=74.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...++++|||+|||+.+++++|+++|+.||.|..+.+..+..++.++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~-----g~~~~g~   95 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVN-----GYKLYGK   95 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHST-----TCBCSSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhC-----CCEeCCc
Confidence            34567899999999999999999999999999543332222368899999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        96 ~l~v~~a~~~~  106 (115)
T 2cpx_A           96 ILVIEFGKNKK  106 (115)
T ss_dssp             BCEEEECCCCS
T ss_pred             EEEEEEccCCC
Confidence            99999998764

>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

Probab=99.59  E-value=9.8e-15  Score=124.43  Aligned_cols=85  Identities=26%  Similarity=0.389  Sum_probs=78.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+.  ++..|.|+.|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999  5789999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus        89 ~a~~~~~   95 (103)
T 2cqg_A           89 LPNSKQS   95 (103)
T ss_dssp             CCCTTCC
T ss_pred             ecCCCCc
Confidence            9987654

>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

Probab=99.59  E-value=3.3e-15  Score=125.86  Aligned_cols=79  Identities=16%  Similarity=0.250  Sum_probs=71.4

Q ss_pred             CCCCcEEEEcCCCC-CCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCc--eeCCeeEE
Q 005812          213 KTQKWKLIIRNIPF-KAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQ--KFGKRPIA  289 (676)
Q Consensus       213 ~~~~~~v~V~nLp~-~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~--~~~g~~i~  289 (676)
                      ..+.++|||+|||+ .+++++|+++|++||.|.+|.|+++      +|||||+|.+.++|..|++.|++.  .|.|++|+
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            44678999999999 9999999999999999999999874      489999999999999999998864  59999999


Q ss_pred             EEEecCCC
Q 005812          290 VDWAVPKN  297 (676)
Q Consensus       290 v~~a~~~~  297 (676)
                      |.|+....
T Consensus        86 V~~a~~~~   93 (102)
T 1x4d_A           86 VHLSQKYK   93 (102)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCCC
Confidence            99997654

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

Probab=99.59  E-value=3.7e-15  Score=128.36  Aligned_cols=84  Identities=35%  Similarity=0.531  Sum_probs=77.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      ......++|||+|||.++++++|+++|++||.|..|.++.+.  +.++|||||+|.+.++|++|+..|+|..|.|+.|.|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345677999999999999999999999999999999999885  348999999999999999999999999999999999


Q ss_pred             EEecCC
Q 005812          291 DWAVPK  296 (676)
Q Consensus       291 ~~a~~~  296 (676)
                      .++.++
T Consensus       102 ~~a~~~  107 (109)
T 2err_A          102 NNATAR  107 (109)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            999775

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

Probab=99.59  E-value=3e-15  Score=127.97  Aligned_cols=84  Identities=23%  Similarity=0.417  Sum_probs=76.4

Q ss_pred             CCCCcEEEEcCCCCCC------CHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCe
Q 005812          213 KTQKWKLIIRNIPFKA------KVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKR  286 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~------~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  286 (676)
                      ....++|||+|||+.+      ++++|+.+|++||.|.+|.|++  .+|.++|||||+|.+.++|.+|+..|||..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            3446899999999999      7899999999999999999983  5789999999999999999999999999999998


Q ss_pred             -eEEEEEecCCCC
Q 005812          287 -PIAVDWAVPKNI  298 (676)
Q Consensus       287 -~i~v~~a~~~~~  298 (676)
                       .|.|.++.....
T Consensus        90 ~~l~V~~a~~~~k  102 (105)
T 2nlw_A           90 HTFRVNLFTDFDK  102 (105)
T ss_dssp             CEEEEECSCCCCC
T ss_pred             ceEEEEEcchHhh
Confidence             999999976543

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

Probab=99.59  E-value=9.3e-16  Score=123.19  Aligned_cols=76  Identities=18%  Similarity=0.368  Sum_probs=73.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..++ ..+.|+.|.|.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999998889999999999999999999999988 9999999999987

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

Probab=99.59  E-value=3.1e-15  Score=127.89  Aligned_cols=81  Identities=22%  Similarity=0.262  Sum_probs=74.4

Q ss_pred             CCCCeEEEcCCCCCC------CHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCee
Q 005812          423 ELQNTIFICNLPFDL------DNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIF  496 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~------teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~  496 (676)
                      ..+++|||+|||+.+      ++++|+++|++||.|..|.++  ..+|.++|||||+|.+.++|.+|+..||     |..
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~-----g~~   85 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNAD-----GYK   85 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCS-----SEE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhC-----Ccc
Confidence            346899999999999      789999999999999999887  3578999999999999999999999999     999


Q ss_pred             ecCc-EEEEEEccCc
Q 005812          497 LKGR-QLTVLKALDK  510 (676)
Q Consensus       497 l~gr-~l~v~~a~~k  510 (676)
                      |+|+ +|.|.++...
T Consensus        86 ~~g~~~l~V~~a~~~  100 (105)
T 2nlw_A           86 LDKQHTFRVNLFTDF  100 (105)
T ss_dssp             CSTTCEEEEECSCCC
T ss_pred             cCCCceEEEEEcchH
Confidence            9998 9999998754

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

Probab=99.59  E-value=3.2e-15  Score=127.60  Aligned_cols=81  Identities=22%  Similarity=0.318  Sum_probs=74.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS-FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~-v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ...++|||+|||+.+++++|+++|+.||.|.. |.|+.+ .+++++|||||+|.+.++|.+|+.. +     +..|+||.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~-----~~~~~gr~   85 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-H-----KERIGHRY   85 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-T-----TCCSSSSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-C-----cchhCCcE
Confidence            34689999999999999999999999999987 878877 7899999999999999999999987 8     99999999


Q ss_pred             EEEEEccCc
Q 005812          502 LTVLKALDK  510 (676)
Q Consensus       502 l~v~~a~~k  510 (676)
                      |.|.++.++
T Consensus        86 i~v~~~~~~   94 (104)
T 1wg5_A           86 IEIFKSSRA   94 (104)
T ss_dssp             CEEEEECTT
T ss_pred             EEEEECCHH
Confidence            999998654

>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

Probab=99.59  E-value=1.5e-15  Score=129.79  Aligned_cols=81  Identities=23%  Similarity=0.393  Sum_probs=71.4

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          422 DELQNTIFICNLPFD-LDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~-~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ..++++|||+|||++ +++++|+++|++||.|.+|+|++      ++|||||+|.+.++|.+|+..|+..   +..|.||
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~---~~~l~Gr   92 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKK---ALWFQGR   92 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHS---CCCSSSS
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccC---CceECCE
Confidence            456789999999998 99999999999999999998863      4799999999999999999988611   4679999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      +|.|.++..+.
T Consensus        93 ~l~V~~a~~~~  103 (112)
T 1x4f_A           93 CVKVDLSEKYK  103 (112)
T ss_dssp             CCEEEEECSCS
T ss_pred             EEEEEECcccc
Confidence            99999997654

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

Probab=99.59  E-value=7.3e-15  Score=125.34  Aligned_cols=84  Identities=29%  Similarity=0.417  Sum_probs=77.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEE-EEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWN-VYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~-v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      .....++|||+|||+.+++++|+++|+.||.|.. |.|+.+ .+|+++|||||+|.+.++|++|+.. ++..+.|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEE
Confidence            3456789999999999999999999999999987 888888 6899999999999999999999997 999999999999


Q ss_pred             EEecCCC
Q 005812          291 DWAVPKN  297 (676)
Q Consensus       291 ~~a~~~~  297 (676)
                      .++.++.
T Consensus        89 ~~~~~~~   95 (104)
T 1wg5_A           89 FKSSRAE   95 (104)
T ss_dssp             EEECTTT
T ss_pred             EECCHHH
Confidence            9987654

>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

Probab=99.59  E-value=7.7e-15  Score=135.33  Aligned_cols=86  Identities=24%  Similarity=0.442  Sum_probs=81.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.+..
T Consensus       115 ~a~~~~  120 (156)
T 1h2v_Z          115 WDAGFK  120 (156)
T ss_dssp             EESCCC
T ss_pred             ECCCCC
Confidence            997754

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=1.3e-14  Score=122.37  Aligned_cols=80  Identities=20%  Similarity=0.332  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHh--CCceeCCeeEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF--NGQKFGKRPIAV  290 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l--~~~~~~g~~i~v  290 (676)
                      ..+.++|||+|||+.+++++|+++|++||.|.+|.++++      +|||||+|.+.++|..|++.|  ++..+.|+.|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            456789999999999999999999999999999998873      699999999999999999976  467899999999


Q ss_pred             EEecCCCC
Q 005812          291 DWAVPKNI  298 (676)
Q Consensus       291 ~~a~~~~~  298 (676)
                      .|+.++..
T Consensus        86 ~~a~~~~~   93 (101)
T 2cq1_A           86 QYSNHKEL   93 (101)
T ss_dssp             EECSCSSC
T ss_pred             EEcCcccC
Confidence            99987654

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

Probab=99.59  E-value=6.5e-16  Score=128.23  Aligned_cols=81  Identities=31%  Similarity=0.497  Sum_probs=74.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      ++|||+|||.++++++|+++|+.||.|.+|.++.++.+|.++|||||+|.+.+ |.+|+..|||..+.|+.|.|.++.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            58999999999999999999999999999999999888999999999999999 99999999999999999999999776


Q ss_pred             CC
Q 005812          297 NI  298 (676)
Q Consensus       297 ~~  298 (676)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=4.7e-15  Score=125.83  Aligned_cols=83  Identities=24%  Similarity=0.344  Sum_probs=75.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+++++++|+++|+.||.+ +|.|+.++ +++++|||||+|.+.++|++||+ +|+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            44567899999999999999999999999955 99999997 89999999999999999999996 79999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      ++.+..
T Consensus        88 ~~~~~~   93 (102)
T 1wez_A           88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            987654

>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

Probab=99.59  E-value=2.7e-15  Score=127.39  Aligned_cols=81  Identities=12%  Similarity=0.274  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..++++|||+|||+.+++++|+++|++||.|..|.++++      +|||||+|.+.++|.+|+..|+..   +..|+|++
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~---~~~i~Gr~   82 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADV---PVYIAGQQ   82 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHS---CCBSSSSB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccC---CceECCEE
Confidence            345689999999999999999999999999999987643      799999999999999999988711   35699999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.|+.++.
T Consensus        83 l~V~~a~~~~   92 (104)
T 1wex_A           83 AFFNYSTSKR   92 (104)
T ss_dssp             CEEEECSSSS
T ss_pred             EEEEEccCcc
Confidence            9999998754

>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

Probab=99.58  E-value=8.4e-15  Score=127.35  Aligned_cols=84  Identities=25%  Similarity=0.521  Sum_probs=78.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee--------
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF--------  283 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~--------  283 (676)
                      .....++|||+|||+++++++|+++|+.||.|..|.|+.++ ++.++|||||+|.+.++|.+|+..|||..|        
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            34567899999999999999999999999999999999998 899999999999999999999999999999        


Q ss_pred             CCeeEEEEEecCC
Q 005812          284 GKRPIAVDWAVPK  296 (676)
Q Consensus       284 ~g~~i~v~~a~~~  296 (676)
                      .+++|.|.|+.|+
T Consensus       100 ~~~~l~v~~a~p~  112 (114)
T 1x5o_A          100 PTEPLLCKFSGPS  112 (114)
T ss_dssp             CSSCBEEEECCCS
T ss_pred             CCCceeEEccCCC
Confidence            5788999999764

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

Probab=99.58  E-value=5.7e-16  Score=128.57  Aligned_cols=80  Identities=31%  Similarity=0.530  Sum_probs=73.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      ++|||+|||..+++++|+++|++||.|..+.++.++.++.++|||||+|.+.+ |.+|+..||     |..++|+.|.|.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~-----g~~~~g~~l~V~   75 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLD-----NTDFMGRTIRVT   75 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSC-----SSCCSSSSCSEE
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhC-----CCEECCeEEEEE
Confidence            58999999999999999999999999999999999888999999999999999 999999999     999999999999


Q ss_pred             EccCch
Q 005812          506 KALDKK  511 (676)
Q Consensus       506 ~a~~k~  511 (676)
                      +|.++.
T Consensus        76 ~a~~~~   81 (90)
T 2ki2_A           76 EANPKK   81 (90)
T ss_dssp             EC----
T ss_pred             EcCCCC
Confidence            988754

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

Probab=99.58  E-value=4.5e-15  Score=131.23  Aligned_cols=80  Identities=20%  Similarity=0.463  Sum_probs=76.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|+ .||     +..|+|+.|.|
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~-----g~~~~g~~l~V  109 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMD-----ETVFRGRTIKV  109 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTT-----TCEETTEECEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcC-----CCeECCeEEEE
Confidence            589999999999999999999999999999999999889999999999999999999999 899     99999999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      .++.+.
T Consensus       110 ~~a~~~  115 (124)
T 2jwn_A          110 LPKRTN  115 (124)
T ss_dssp             EESSCC
T ss_pred             EECCCC
Confidence            998754

>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*

Probab=99.58  E-value=8.8e-16  Score=164.77  Aligned_cols=83  Identities=17%  Similarity=0.413  Sum_probs=79.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      +.++|||+|||+.+|+++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|.+||..||     |..|+|+.|.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~ln-----g~~i~gr~i~  175 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHAD-----GKKIDGRRVL  175 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcC-----CCEECCEEEE
Confidence            35799999999999999999999999999999999998899999999999999999999999999     9999999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.++.++.
T Consensus       176 V~~a~~~~  183 (437)
T 3pgw_S          176 VDVERGRT  183 (437)
T ss_pred             EEEeCCCC
Confidence            99998754

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=2.6e-15  Score=130.65  Aligned_cols=81  Identities=26%  Similarity=0.397  Sum_probs=77.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      .++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|++|+ .|||..|.|+.|.|.|+.+
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            479999999999999999999999999999999999988999999999999999999999 8999999999999999876


Q ss_pred             CC
Q 005812          296 KN  297 (676)
Q Consensus       296 ~~  297 (676)
                      +.
T Consensus       104 ~~  105 (114)
T 2cq4_A          104 EK  105 (114)
T ss_dssp             HH
T ss_pred             Cc
Confidence            53

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

Probab=99.58  E-value=1.2e-15  Score=136.16  Aligned_cols=84  Identities=20%  Similarity=0.401  Sum_probs=79.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEE--EEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCc----eeCCe
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWN--VYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQ----KFGKR  286 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~--v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~----~~~g~  286 (676)
                      ....++|||+|||+++++++|+++|++||.|..  |+|++++.+|+++|||||+|.+. +|.+|+..|||.    .|.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            456789999999999999999999999999977  99999999999999999999999 999999999999    99999


Q ss_pred             eEEEEEecCCC
Q 005812          287 PIAVDWAVPKN  297 (676)
Q Consensus       287 ~i~v~~a~~~~  297 (676)
                      .|.|.|+.+..
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999997754

>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

Probab=99.58  E-value=1e-14  Score=125.69  Aligned_cols=83  Identities=22%  Similarity=0.415  Sum_probs=76.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||.++++++|+++|++||.|..|.|+.+   +.++|||||+|.+.++|++|++.||+..|.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            4456789999999999999999999999999999999764   4588999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.++.
T Consensus        95 ~a~~~~  100 (109)
T 1x4a_A           95 FPRSGR  100 (109)
T ss_dssp             CCCCCC
T ss_pred             EcccCC
Confidence            997764

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

Probab=99.58  E-value=5.5e-15  Score=128.96  Aligned_cols=82  Identities=18%  Similarity=0.369  Sum_probs=78.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      .++|||+|||+.+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+.. ++..|.|+.|.|.++.+
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCC
Confidence            48999999999999999999999999999999999988999999999999999999999997 99999999999999987


Q ss_pred             CCC
Q 005812          296 KNI  298 (676)
Q Consensus       296 ~~~  298 (676)
                      +..
T Consensus       106 ~~~  108 (116)
T 1x4b_A          106 REE  108 (116)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            754

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

Probab=99.58  E-value=1.5e-15  Score=121.97  Aligned_cols=77  Identities=25%  Similarity=0.439  Sum_probs=72.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      ++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|+..++      ..++|++|.|.
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~------~~~~g~~l~v~   74 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR------HELDSKTIDPK   74 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT------CCCSSCCCEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC------CccCCEEEEEE
Confidence            479999999999999999999999999999999998889999999999999999999999886      78999999999


Q ss_pred             Ecc
Q 005812          506 KAL  508 (676)
Q Consensus       506 ~a~  508 (676)
                      +|.
T Consensus        75 ~a~   77 (77)
T 1uaw_A           75 VAF   77 (77)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            873

>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

Probab=99.58  E-value=9e-15  Score=124.11  Aligned_cols=81  Identities=12%  Similarity=0.119  Sum_probs=72.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCc--eeCCeeEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQ--KFGKRPIA  289 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~--~~~g~~i~  289 (676)
                      ...+.++|||+|||+.+++++|+++|++||.|.+|.+++      .+|||||+|.+.++|.+|++.|++.  .+.|+.|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            345678999999999999999999999999999999886      3699999999999999999988654  58999999


Q ss_pred             EEEecCCCC
Q 005812          290 VDWAVPKNI  298 (676)
Q Consensus       290 v~~a~~~~~  298 (676)
                      |.|+.++..
T Consensus        85 V~~a~~~~~   93 (104)
T 1wex_A           85 FNYSTSKRI   93 (104)
T ss_dssp             EEECSSSSC
T ss_pred             EEEccCccc
Confidence            999977653

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=7.7e-15  Score=126.81  Aligned_cols=81  Identities=19%  Similarity=0.361  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCC--ceeCCeeEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG--QKFGKRPIA  289 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~--~~~~g~~i~  289 (676)
                      ...+.++|||+|||+++++++|+++|++||.|.+|.|+++      +|||||+|.+.++|.+|++.|++  ..|.|++|.
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            3446789999999999999999999999999999999874      69999999999999999998874  679999999


Q ss_pred             EEEecCCCC
Q 005812          290 VDWAVPKNI  298 (676)
Q Consensus       290 v~~a~~~~~  298 (676)
                      |.|+.++..
T Consensus       101 V~~a~~k~~  109 (119)
T 2ad9_A          101 IQFSNHKEL  109 (119)
T ss_dssp             EEECSSSSC
T ss_pred             EEEccCCCC
Confidence            999987654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=9e-15  Score=124.16  Aligned_cols=81  Identities=17%  Similarity=0.282  Sum_probs=73.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+.+++++|+++|++||.|   +++.+ .++.++|||||+|.+.++|.+|+..||     +..|.|+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~   82 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCN-----KREIEGRA   82 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTS-----SEEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhC-----CCEeCCeE
Confidence            3356899999999999999999999999987   45555 678899999999999999999999999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        83 l~v~~a~~~~   92 (101)
T 2fc9_A           83 IRLELQGPRG   92 (101)
T ss_dssp             EEEEECSSCC
T ss_pred             EEEEEcCCCC
Confidence            9999998763

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

Probab=99.57  E-value=6.2e-15  Score=130.32  Aligned_cols=81  Identities=20%  Similarity=0.377  Sum_probs=77.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      .++|||+|||.++++++|+++|+.||.|.+|.++.++.++.++|||||+|.+.++|.+|+ .|+|..|.|+.|.|.|+.+
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            579999999999999999999999999999999999889999999999999999999999 7999999999999999876


Q ss_pred             CC
Q 005812          296 KN  297 (676)
Q Consensus       296 ~~  297 (676)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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

Probab=99.57  E-value=1.2e-14  Score=125.06  Aligned_cols=76  Identities=20%  Similarity=0.218  Sum_probs=71.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC----
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG----  499 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g----  499 (676)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.+       |||||+|.+.++|.+|++.||     +..|.|    
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~-----g~~~~g~~~~   81 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLD-----NTKFRSHEGE   81 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSS-----SEEEECTTSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHC-----cCCccCCcCc
Confidence            4689999999999999999999999999999988755       899999999999999999999     999999    


Q ss_pred             -cEEEEEEccCch
Q 005812          500 -RQLTVLKALDKK  511 (676)
Q Consensus       500 -r~l~v~~a~~k~  511 (676)
                       +.|.|.++.++.
T Consensus        82 ~~~i~V~~a~~~~   94 (108)
T 1x4c_A           82 TAYIRVKVDGPRS   94 (108)
T ss_dssp             EEEEEEEESSCCS
T ss_pred             ceEEEEEeCCCCC
Confidence             999999998864

>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

Probab=99.57  E-value=9.9e-15  Score=122.72  Aligned_cols=77  Identities=19%  Similarity=0.434  Sum_probs=70.9

Q ss_pred             CCCCCCeEEEcCCCC-CCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          421 EDELQNTIFICNLPF-DLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~-~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      ...++++|||+|||+ .+++++|+++|+.||.|..+.+        ++|||||+|.+.++|.+|+..||     |..++|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~Ai~~l~-----g~~~~g   84 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEXES-----QEMNFG   84 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE--------CSSEEEEEESSHHHHHHHHHHHT-----TSEETT
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE--------eCCEEEEEECCHHHHHHHHHHcC-----CCEECC
Confidence            445678999999998 9999999999999999999987        27899999999999999999999     999999


Q ss_pred             cEEEEEEccCc
Q 005812          500 RQLTVLKALDK  510 (676)
Q Consensus       500 r~l~v~~a~~k  510 (676)
                      +.|.|.++.++
T Consensus        85 ~~l~V~~a~~~   95 (97)
T 2xnq_A           85 KKLILEVSSSN   95 (97)
T ss_dssp             EECEEEECCCC
T ss_pred             EEEEEEecCCC
Confidence            99999998765

>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

Probab=99.57  E-value=4e-15  Score=129.31  Aligned_cols=84  Identities=20%  Similarity=0.246  Sum_probs=78.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCce-EEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLV-WNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i-~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      .....++|||+|||+++++++|+++|+.||.| ..|.|+.++ +|+++|||||+|.+.++|.+||+. |+..|.|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v   88 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            34567899999999999999999999999999 889999998 899999999999999999999997 999999999999


Q ss_pred             EEecCCC
Q 005812          291 DWAVPKN  297 (676)
Q Consensus       291 ~~a~~~~  297 (676)
                      .++.++.
T Consensus        89 ~~a~~~~   95 (114)
T 2cpy_A           89 HVVTLED   95 (114)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9997654

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

Probab=99.57  E-value=7.9e-15  Score=132.64  Aligned_cols=82  Identities=30%  Similarity=0.446  Sum_probs=77.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|+|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             Ee
Q 005812          292 WA  293 (676)
Q Consensus       292 ~a  293 (676)
                      ||
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            85

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.57  E-value=5.4e-15  Score=126.83  Aligned_cols=78  Identities=22%  Similarity=0.184  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCC-ceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFG-EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G-~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      ..++|||+|||+++++++|+++|++|| .|..+.++.+    .++|||||+|.+.++|.+|+..||     |..|+|+.|
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~ln-----g~~l~Gr~i   97 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLN-----NIEFRGSVI   97 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTT-----TEEETTEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcC-----CCEECCeEE
Confidence            357999999999999999999999999 8999987532    479999999999999999999999     999999999


Q ss_pred             EEEEccCc
Q 005812          503 TVLKALDK  510 (676)
Q Consensus       503 ~v~~a~~k  510 (676)
                      .|.++..+
T Consensus        98 ~V~~a~~~  105 (111)
T 2jvr_A           98 TVERDDNP  105 (111)
T ss_dssp             EEEESCC-
T ss_pred             EEEECCCC
Confidence            99998754

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

Probab=99.57  E-value=6.9e-15  Score=129.55  Aligned_cols=84  Identities=15%  Similarity=0.330  Sum_probs=75.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH----HhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCee
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIK----DMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRP  287 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~----~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  287 (676)
                      ...+.++|||+|||+.+++++|+    ++|++||.|.+|.+..   +++++|||||+|.+.++|..|+..|||..|.|+.
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~  101 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNP  101 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCE
Confidence            34557899999999999999876    6999999999998864   5778999999999999999999999999999999


Q ss_pred             EEEEEecCCCC
Q 005812          288 IAVDWAVPKNI  298 (676)
Q Consensus       288 i~v~~a~~~~~  298 (676)
                      |.|.|+.++..
T Consensus       102 l~V~~a~~~~~  112 (127)
T 2a3j_A          102 LVITFSETPQS  112 (127)
T ss_dssp             CEEEECCCCCH
T ss_pred             EEEEEccCcch
Confidence            99999987643

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

Probab=99.57  E-value=9.8e-15  Score=119.62  Aligned_cols=76  Identities=25%  Similarity=0.443  Sum_probs=70.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHc-CCCCCCCeeecCc
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS-KTTSGLGIFLKGR  500 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l-~~~~~~g~~l~gr  500 (676)
                      ..+.++|||+|||..+++++|+++|++||.|..+.++.+      +|||||+|.+.++|.+|+..| +     +..++|+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~-----~~~~~g~   77 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFN-----KLIVNGR   77 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTT-----TCEETTE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcC-----CeeECCC
Confidence            345689999999999999999999999999999988753      799999999999999999999 8     9999999


Q ss_pred             EEEEEEcc
Q 005812          501 QLTVLKAL  508 (676)
Q Consensus       501 ~l~v~~a~  508 (676)
                      +|.|.||+
T Consensus        78 ~l~v~~ak   85 (85)
T 2ytc_A           78 RLNVKWGR   85 (85)
T ss_dssp             ECCEEECC
T ss_pred             EEEEEecC
Confidence            99999974

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.57  E-value=9e-16  Score=130.40  Aligned_cols=82  Identities=20%  Similarity=0.261  Sum_probs=75.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .+.++|||+|||+.+++++|+++|+.||.|.. .++.+..++.++|||||+|.+.++|.+|++ ||     +..|.|+.|
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~-----g~~~~g~~l   87 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LT-----GLKVFGNEI   87 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GG-----GCCBTTBCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cC-----CcEECCcEE
Confidence            34689999999999999999999999999988 567777788999999999999999999998 99     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        88 ~V~~a~~~~   96 (101)
T 1fj7_A           88 KLEKPKGRD   96 (101)
T ss_dssp             EEECCSCCC
T ss_pred             EEEEcCCCC
Confidence            999998764

>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

Probab=99.57  E-value=8.3e-15  Score=123.35  Aligned_cols=80  Identities=19%  Similarity=0.304  Sum_probs=72.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec--
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK--  498 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~--  498 (676)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|++.||     +..|.  
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~-----g~~~~~~   81 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMR-----GFPLGGP   81 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHT-----TCBCSSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHC-----CCEeCCC
Confidence            3345689999999999999999999999999999987643      7899999999999999999999     99999  


Q ss_pred             CcEEEEEEccCch
Q 005812          499 GRQLTVLKALDKK  511 (676)
Q Consensus       499 gr~l~v~~a~~k~  511 (676)
                      |++|.|.++.++.
T Consensus        82 g~~l~V~~a~~~~   94 (97)
T 1why_A           82 DRRLRVDFAKSGP   94 (97)
T ss_dssp             SCBCEEEECCCCC
T ss_pred             CcEEEEEECCCCC
Confidence            9999999998763

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=2e-14  Score=122.04  Aligned_cols=83  Identities=24%  Similarity=0.513  Sum_probs=74.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|++||.|   .++.+ .++.++|||||+|.+.++|++|+..||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            44567999999999999999999999999977   56666 578899999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus        87 ~a~~~~~   93 (101)
T 2fc9_A           87 LQGPRGS   93 (101)
T ss_dssp             ECSSCCC
T ss_pred             EcCCCCC
Confidence            9987643

>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}

Probab=99.56  E-value=1.6e-15  Score=130.17  Aligned_cols=84  Identities=14%  Similarity=0.201  Sum_probs=77.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCc---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGE---VVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK  498 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~---v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~  498 (676)
                      ....++|||+|||+++++++|+++|+.||.   |..|.|+.+.. |+++|||||+|.+.++|.+|+. ++     +..|+
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~-----~~~~~   80 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KH-----RMYMG   80 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TT-----TCCSS
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hC-----cceeC
Confidence            345689999999999999999999999998   89999999876 9999999999999999999998 99     99999


Q ss_pred             CcEEEEEEccCchh
Q 005812          499 GRQLTVLKALDKKL  512 (676)
Q Consensus       499 gr~l~v~~a~~k~~  512 (676)
                      ||.|.|.++.+++.
T Consensus        81 gr~i~V~~a~~~~~   94 (107)
T 2lmi_A           81 QRYVEVYEINNEDV   94 (107)
T ss_dssp             SSCCCCEECCHHHH
T ss_pred             CeEEEEEECCHHHH
Confidence            99999999876553

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

Probab=99.56  E-value=1.2e-14  Score=123.54  Aligned_cols=82  Identities=28%  Similarity=0.299  Sum_probs=74.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+.+++++|+++|+.|+   .|.++.+..++.++|||||+|.+.++|.+|+..||     +..|.|+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~   83 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME-----DGEIDGNK   83 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHT-----TCEETTEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhC-----CCeECCeE
Confidence            44568999999999999999999999874   56788888889999999999999999999999999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        84 l~V~~a~~~~   93 (102)
T 2fc8_A           84 VTLDWAKPKG   93 (102)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEecCCC
Confidence            9999998764

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

Probab=99.56  E-value=8.6e-15  Score=121.39  Aligned_cols=76  Identities=25%  Similarity=0.391  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .+.++|||+|||..+++++|+++|++||.|..|.++        +|||||+|.+.++|.+|+..||     +..|+|+.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~l   72 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLH-----HYKLHGVNI   72 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHT-----TCBCSSCBC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhc-----CCccCCcEE
Confidence            346899999999999999999999999999999876        6899999999999999999999     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        73 ~v~~a~~~~   81 (90)
T 2dnq_A           73 NVEASKNKS   81 (90)
T ss_dssp             EEECSSCCC
T ss_pred             EEEECCCCC
Confidence            999998764

>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

Probab=99.56  E-value=1.8e-15  Score=120.78  Aligned_cols=75  Identities=25%  Similarity=0.346  Sum_probs=71.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEE
Q 005812          427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLK  506 (676)
Q Consensus       427 ~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~  506 (676)
                      +|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++. +     +..++|+.|.|.+
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~-----~~~~~g~~l~v~~   74 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-K-----YHNVGLSKCEIKV   74 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-S-----SCCBTTBCCCEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-C-----CCeECCEEEEEEE
Confidence            589999999999999999999999999999999988899999999999999999999985 7     8999999999987


Q ss_pred             c
Q 005812          507 A  507 (676)
Q Consensus       507 a  507 (676)
                      |
T Consensus        75 a   75 (75)
T 1iqt_A           75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            5

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

Probab=99.56  E-value=1.8e-14  Score=119.51  Aligned_cols=79  Identities=30%  Similarity=0.382  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||.++++++|+++|++||.|..|.++        +|||||+|.+.++|.+|+..||+..+.|+.|+|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   75 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVE   75 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEE
Confidence            45567899999999999999999999999999999997        4799999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus        76 ~a~~~~~   82 (90)
T 2dnq_A           76 ASKNKSK   82 (90)
T ss_dssp             CSSCCCC
T ss_pred             ECCCCCC
Confidence            9987653

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.56  E-value=8e-15  Score=128.09  Aligned_cols=82  Identities=20%  Similarity=0.354  Sum_probs=76.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCc---eEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGL---VWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIA  289 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~---i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~  289 (676)
                      ....++|||+|||+++++++|+++|+.||.   |..|+|+.++. |+++|||||+|.+.++|++|++ +|+..|.|+.|.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            445789999999999999999999999999   89999999875 9999999999999999999999 899999999999


Q ss_pred             EEEecCC
Q 005812          290 VDWAVPK  296 (676)
Q Consensus       290 v~~a~~~  296 (676)
                      |.++.++
T Consensus        92 V~~a~~~   98 (118)
T 2db1_A           92 VFKSHRT   98 (118)
T ss_dssp             EEEECHH
T ss_pred             EEECCHH
Confidence            9998654

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.56  E-value=5e-15  Score=132.00  Aligned_cols=83  Identities=19%  Similarity=0.335  Sum_probs=77.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCc---eEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGL---VWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPI  288 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~---i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i  288 (676)
                      .....++|||+|||+++|+++|+++|+.||.   |.+|.|+.++. |+++|||||+|.+.++|++|++ ||+..|.|+.|
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i  117 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI  117 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEE
Confidence            3456789999999999999999999999999   88999999976 9999999999999999999999 99999999999


Q ss_pred             EEEEecCC
Q 005812          289 AVDWAVPK  296 (676)
Q Consensus       289 ~v~~a~~~  296 (676)
                      .|.++.++
T Consensus       118 ~V~~a~~~  125 (136)
T 2hgl_A          118 EVFKSHRT  125 (136)
T ss_dssp             EEEECCHH
T ss_pred             EEEECChH
Confidence            99998654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=1.2e-14  Score=122.43  Aligned_cols=80  Identities=26%  Similarity=0.407  Sum_probs=71.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ....++|||+|||+.+++++|+++|+.||.|. +.++.+    .++|||||+|.+.++|.+|+..||     |..|+|+.
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~   85 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQ-----GLRLGTDT   85 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHT-----TCCSSSSC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhC-----CCEECCcE
Confidence            34468999999999999999999999999997 666654    578999999999999999999999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        86 l~V~~a~~~~   95 (97)
T 2e5j_A           86 LRVALARQQR   95 (97)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEcCCCC
Confidence            9999998753

>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

Probab=99.56  E-value=8.7e-15  Score=123.73  Aligned_cols=79  Identities=28%  Similarity=0.413  Sum_probs=72.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++++      +|||||+|.+.++|.+|++.|+     +..|.|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~-----g~~~~g~~   80 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELD-----NMPLRGKQ   80 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHT-----TCCBTTBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhC-----CCEeCCce
Confidence            345689999999999999999999999999999988743      7899999999999999999999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        81 l~v~~a~~~~   90 (99)
T 2cpj_A           81 LRVRFACHSA   90 (99)
T ss_dssp             CEEEESSCCS
T ss_pred             EEEEEcCCCC
Confidence            9999998753

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=5e-15  Score=129.57  Aligned_cols=83  Identities=23%  Similarity=0.296  Sum_probs=74.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCce----eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEV----VSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v----~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      ..++|||+|||+++|+++|+++|+.||.|    ..|.|+.+ .+|+++|||||+|.+.++|.+|+.. |     +..|+|
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~-----~~~l~g   94 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-H-----KDLLGK   94 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-T-----TEESSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-C-----CCeeCC
Confidence            35799999999999999999999999875    68989888 5899999999999999999999986 8     899999


Q ss_pred             cEEEEEEccCchhh
Q 005812          500 RQLTVLKALDKKLA  513 (676)
Q Consensus       500 r~l~v~~a~~k~~~  513 (676)
                      |.|.|..+.+++..
T Consensus        95 R~i~V~~a~~~e~~  108 (123)
T 2dha_A           95 RYIELFRSTAAEVQ  108 (123)
T ss_dssp             CEECCEEECHHHHH
T ss_pred             eEEEEEECCHHHHH
Confidence            99999998765433

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

Probab=99.55  E-value=1.4e-14  Score=118.68  Aligned_cols=78  Identities=19%  Similarity=0.345  Sum_probs=72.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHh-CCceeCCeeEE
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF-NGQKFGKRPIA  289 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l-~~~~~~g~~i~  289 (676)
                      ......++|||+|||..+++++|+++|++||.|..|.+++      ++|||||+|.+.++|.+|++.| ++..+.|+.|.
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~------~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~   80 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ------RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLN   80 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECC
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC------CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEE
Confidence            3445678999999999999999999999999999999987      4799999999999999999998 99999999999


Q ss_pred             EEEec
Q 005812          290 VDWAV  294 (676)
Q Consensus       290 v~~a~  294 (676)
                      |.|++
T Consensus        81 v~~ak   85 (85)
T 2ytc_A           81 VKWGR   85 (85)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99973

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.55  E-value=3.7e-15  Score=120.93  Aligned_cols=72  Identities=26%  Similarity=0.517  Sum_probs=67.6

Q ss_pred             cEEEEcCCCCCC------CHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCe-eEE
Q 005812          217 WKLIIRNIPFKA------KVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKR-PIA  289 (676)
Q Consensus       217 ~~v~V~nLp~~~------~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~-~i~  289 (676)
                      ++|||+|||..+      ++++|+++|++||.|.+|.+++  .+|+++|||||+|.+.++|.+|++.|||..|.|+ .|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      7799999999999999999883  5789999999999999999999999999999999 887


Q ss_pred             E
Q 005812          290 V  290 (676)
Q Consensus       290 v  290 (676)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>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

Probab=99.55  E-value=7.3e-15  Score=125.52  Aligned_cols=80  Identities=18%  Similarity=0.233  Sum_probs=71.8

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhC--CceeCCeeEE
Q 005812          213 KTQKWKLIIRNIPFK-AKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN--GQKFGKRPIA  289 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~-~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~--~~~~~g~~i~  289 (676)
                      ..+.++|||+|||++ +++++|+++|++||.|.+|.|++      ++|||||+|.+.++|..|++.|+  +..|.|+.|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            446789999999998 99999999999999999999975      57999999999999999999886  4569999999


Q ss_pred             EEEecCCCC
Q 005812          290 VDWAVPKNI  298 (676)
Q Consensus       290 v~~a~~~~~  298 (676)
                      |.|+.++..
T Consensus        96 V~~a~~~~~  104 (112)
T 1x4f_A           96 VDLSEKYKK  104 (112)
T ss_dssp             EEEECSCSS
T ss_pred             EEECccccc
Confidence            999976653

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.55  E-value=2.9e-15  Score=121.60  Aligned_cols=72  Identities=24%  Similarity=0.315  Sum_probs=67.0

Q ss_pred             CeEEEcCCCCCC------CHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          426 NTIFICNLPFDL------DNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       426 ~~l~V~nLp~~~------teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      ++|||+|||+.+      ++++|+++|++||.|..|.++  ..+|.++|||||+|.+.++|.+|+..||     |..|+|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~ln-----g~~~~g   74 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNAD-----GYKLDK   74 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSS-----SCCCSS
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhc-----CcccCC
Confidence            689999999999      779999999999999999877  3578999999999999999999999999     999999


Q ss_pred             c-EEEE
Q 005812          500 R-QLTV  504 (676)
Q Consensus       500 r-~l~v  504 (676)
                      + +|.|
T Consensus        75 ~~~l~V   80 (81)
T 2krb_A           75 QHTFRV   80 (81)
T ss_dssp             SSCCCC
T ss_pred             ceeEEe
Confidence            9 8876

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.55  E-value=7.3e-15  Score=125.98  Aligned_cols=80  Identities=14%  Similarity=0.216  Sum_probs=72.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCC-ceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVG-LVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G-~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      ....++|||+|||+++++++|+++|+.|| .|..+.++.+    .++|||||+|.+.++|++|++.|||..|.|+.|.|.
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~  100 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE  100 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            44578999999999999999999999999 8999998643    378999999999999999999999999999999999


Q ss_pred             EecCC
Q 005812          292 WAVPK  296 (676)
Q Consensus       292 ~a~~~  296 (676)
                      ++...
T Consensus       101 ~a~~~  105 (111)
T 2jvr_A          101 RDDNP  105 (111)
T ss_dssp             ESCC-
T ss_pred             ECCCC
Confidence            98654

>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

Probab=99.55  E-value=1.3e-14  Score=122.65  Aligned_cols=81  Identities=23%  Similarity=0.418  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|++||.|..|.+++      .+|||||+|.+.++|.+|++.|+|..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~------~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET------TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            455678999999999999999999999999999999986      46899999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus        85 ~a~~~~~   91 (99)
T 2cpj_A           85 FACHSAS   91 (99)
T ss_dssp             ESSCCSC
T ss_pred             EcCCCCC
Confidence            9987653

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

Probab=99.55  E-value=7.5e-15  Score=124.65  Aligned_cols=76  Identities=25%  Similarity=0.382  Sum_probs=71.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      .+++|||+|||..+++++|+++|+.||.|..++++      .++|||||+|.+.++|.+|+..||     |..|+|+.|.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~-----g~~~~g~~l~   94 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALA-----NFPFQGRNLR   94 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHT-----TCEETTEECC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhC-----CCeECCeEEE
Confidence            46899999999999999999999999999999886      358999999999999999999999     9999999999


Q ss_pred             EEEccCc
Q 005812          504 VLKALDK  510 (676)
Q Consensus       504 v~~a~~k  510 (676)
                      |.|+.++
T Consensus        95 V~~a~~~  101 (101)
T 2la4_A           95 TGWGKER  101 (101)
T ss_dssp             CCBCCCC
T ss_pred             EEeccCC
Confidence            9998764

>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* ...

Probab=99.55  E-value=5.6e-15  Score=124.44  Aligned_cols=83  Identities=25%  Similarity=0.416  Sum_probs=75.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee
Q 005812          422 DELQNTIFICNLPFDLDNEEVK----QRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL  497 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~----~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l  497 (676)
                      ..++++|||+|||..+++++|+    ++|++||.|..|.++.   ++.++|||||+|.+.++|.+|+..||     |..|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~-----g~~~   76 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQ-----GFPF   76 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHT-----TCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhC-----CCEE
Confidence            3456899999999999999999    9999999999998763   46778999999999999999999999     9999


Q ss_pred             cCcEEEEEEccCchh
Q 005812          498 KGRQLTVLKALDKKL  512 (676)
Q Consensus       498 ~gr~l~v~~a~~k~~  512 (676)
                      +|+.|.|.++.++..
T Consensus        77 ~g~~l~v~~a~~~~~   91 (97)
T 1nu4_A           77 YDKPMRIQYAKTDSD   91 (97)
T ss_dssp             TTEECEEEECSSCCT
T ss_pred             CCcEEEEEEccCCCc
Confidence            999999999988654

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

Probab=99.55  E-value=2.2e-14  Score=122.01  Aligned_cols=84  Identities=25%  Similarity=0.457  Sum_probs=76.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||.++++++|+++|+.|+   .|.++.++.++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            455678999999999999999999999874   57778887889999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus        88 ~a~~~~~   94 (102)
T 2fc8_A           88 WAKPKGE   94 (102)
T ss_dssp             ECCCCCS
T ss_pred             EecCCCC
Confidence            9987653

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

Probab=99.55  E-value=1.1e-14  Score=125.00  Aligned_cols=78  Identities=21%  Similarity=0.405  Sum_probs=72.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      .....++|||+|||+.+++++|+++|++||.|..|.++        +|||||+|.+.++|.+|+..||     |..|+|+
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~-----g~~~~g~   93 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVH-----GKSFANQ   93 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHT-----TCEETTE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcC-----CCEECCe
Confidence            44556899999999999999999999999999999886        7899999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.++.++.
T Consensus        94 ~l~V~~a~~~~  104 (108)
T 2jvo_A           94 PLEVVYSKLPA  104 (108)
T ss_dssp             ECEEESCSCCC
T ss_pred             EEEEEEecCCC
Confidence            99999988754

>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

Probab=99.55  E-value=2.1e-14  Score=123.50  Aligned_cols=79  Identities=23%  Similarity=0.374  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC-----e
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK-----R  286 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g-----~  286 (676)
                      .....++|||+|||+++++++|+++|+.||.|..|.|+.+       |||||+|.+.++|++||+.||+..|.|     +
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~   83 (108)
T 1x4c_A           11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   83 (108)
T ss_dssp             CCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcce
Confidence            4456789999999999999999999999999999999875       899999999999999999999999999     9


Q ss_pred             eEEEEEecCCC
Q 005812          287 PIAVDWAVPKN  297 (676)
Q Consensus       287 ~i~v~~a~~~~  297 (676)
                      .|.|.++.++.
T Consensus        84 ~i~V~~a~~~~   94 (108)
T 1x4c_A           84 YIRVKVDGPRS   94 (108)
T ss_dssp             EEEEEESSCCS
T ss_pred             EEEEEeCCCCC
Confidence            99999998764

>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

Probab=99.55  E-value=1.3e-14  Score=125.04  Aligned_cols=79  Identities=22%  Similarity=0.400  Sum_probs=73.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ....++|||+|||..+++++|+++|+.||.|..|.++.+      +|||||+|.+.++|.+|+..|+     +..|+|+.
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~   90 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVN-----GTTIEGHV   90 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHT-----TCEETTEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcC-----CCEECCcE
Confidence            344689999999999999999999999999999988765      7899999999999999999999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.|+.++.
T Consensus        91 l~v~~a~~~~  100 (109)
T 1x4g_A           91 VKCYWGKESP  100 (109)
T ss_dssp             CEEECCCCCC
T ss_pred             EEEEecCCCC
Confidence            9999998764

>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

Probab=99.55  E-value=1.8e-14  Score=121.33  Aligned_cols=80  Identities=18%  Similarity=0.327  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC--CeeEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG--KRPIA  289 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~--g~~i~  289 (676)
                      .....++|||+|||..+++++|+++|++||.|.+|.++.+      +|||||+|.+.++|++|++.||+..+.  |+.|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~   86 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEE
Confidence            3456689999999999999999999999999999999863      689999999999999999999999999  99999


Q ss_pred             EEEecCCC
Q 005812          290 VDWAVPKN  297 (676)
Q Consensus       290 v~~a~~~~  297 (676)
                      |.|+.++.
T Consensus        87 V~~a~~~~   94 (97)
T 1why_A           87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99998764

>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

Probab=99.55  E-value=4e-15  Score=131.46  Aligned_cols=84  Identities=23%  Similarity=0.340  Sum_probs=76.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||+.+++++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|.+||. ||+..|.|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            4456899999999999999999999999999886666666789999999999999999999999 999999999999999


Q ss_pred             ecCCC
Q 005812          293 AVPKN  297 (676)
Q Consensus       293 a~~~~  297 (676)
                      +.++.
T Consensus       101 a~~~~  105 (124)
T 1wel_A          101 ITKKG  105 (124)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            97653

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

Probab=99.55  E-value=3.9e-14  Score=119.72  Aligned_cols=77  Identities=22%  Similarity=0.346  Sum_probs=70.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhC--CceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAF--GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~--G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      ..+.++|||+|||+.+++++|+++|++|  |.|..|.++        +|||||+|.+.++|.+|+..||     +..|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~-----g~~~~g   78 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALN-----GKVLDG   78 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHS-----SEEETT
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhC-----CCEeCC
Confidence            3456899999999999999999999999  999998753        6799999999999999999999     999999


Q ss_pred             cEEEEEEccCch
Q 005812          500 RQLTVLKALDKK  511 (676)
Q Consensus       500 r~l~v~~a~~k~  511 (676)
                      +.|.|.++.++.
T Consensus        79 ~~l~v~~a~~~~   90 (99)
T 2cpd_A           79 SPIEVTLAKPVD   90 (99)
T ss_dssp             EEEEEECCCCCC
T ss_pred             cEEEEEECCCCC
Confidence            999999998764

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

Probab=99.55  E-value=2.7e-14  Score=118.95  Aligned_cols=77  Identities=18%  Similarity=0.356  Sum_probs=70.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++        ++||||+|.+.++|.+|+..||     +..|.|+.
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~-----g~~~~g~~   73 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLD-----NTEFQGKR   73 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHT-----TEEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhC-----CCeeCCcE
Confidence            3456899999999999999999999999999999876        4499999999999999999999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        74 l~V~~a~~~~   83 (92)
T 2dgt_A           74 MHVQLSTSRL   83 (92)
T ss_dssp             EEEEESSCCC
T ss_pred             EEEEEccCCC
Confidence            9999998764

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

Probab=99.54  E-value=1.1e-14  Score=124.61  Aligned_cols=80  Identities=25%  Similarity=0.339  Sum_probs=73.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ...+|||+|||+++++++|+++|+.| .|.+|.|+.++. |+++|||||+|.+.++|++|| .+|+..|+|+.|.|..+.
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            35799999999999999999999999 899999999875 899999999999999999999 589999999999999886


Q ss_pred             CCC
Q 005812          295 PKN  297 (676)
Q Consensus       295 ~~~  297 (676)
                      ++.
T Consensus        92 ~~~   94 (109)
T 2dnn_A           92 ERQ   94 (109)
T ss_dssp             HHH
T ss_pred             ccc
Confidence            543

>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* ...

Probab=99.54  E-value=8.7e-15  Score=123.24  Aligned_cols=83  Identities=24%  Similarity=0.430  Sum_probs=75.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH----HhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCee
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIK----DMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRP  287 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~----~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  287 (676)
                      ...+.++|||+|||.++++++|+    ++|++||.|..|.++.   +|.++|||||+|.+.++|..|+..|||..+.|+.
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   80 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcE
Confidence            34567899999999999999999    9999999999999874   5668899999999999999999999999999999


Q ss_pred             EEEEEecCCC
Q 005812          288 IAVDWAVPKN  297 (676)
Q Consensus       288 i~v~~a~~~~  297 (676)
                      |.|.|+.++.
T Consensus        81 l~v~~a~~~~   90 (97)
T 1nu4_A           81 MRIQYAKTDS   90 (97)
T ss_dssp             CEEEECSSCC
T ss_pred             EEEEEccCCC
Confidence            9999997754

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.54  E-value=4.9e-15  Score=126.06  Aligned_cols=81  Identities=25%  Similarity=0.432  Sum_probs=75.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      ..++|||+|||+.+++++|+++|+.||.|..|.++.+. ++.++|||||+|.+.++|.+|+.  +     +..|+|+.|.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~-----~~~~~g~~l~   79 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--S-----QINFHGKKLK   79 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--C-----CCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--C-----CCeECCEEEE
Confidence            35899999999999999999999999999999999997 89999999999999999999998  8     8999999999


Q ss_pred             EEEccCchh
Q 005812          504 VLKALDKKL  512 (676)
Q Consensus       504 v~~a~~k~~  512 (676)
                      |.++.++..
T Consensus        80 v~~a~~~~~   88 (102)
T 2xs2_A           80 LGPAIRKQN   88 (102)
T ss_dssp             EEEEEECC-
T ss_pred             EEECCcCcc
Confidence            999987653

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.54  E-value=2.5e-15  Score=134.39  Aligned_cols=121  Identities=20%  Similarity=0.185  Sum_probs=74.3

Q ss_pred             ceEEEEeCCHHHHHHHHHHhCCCeecCeEEEEec--CCCCCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcc
Q 005812          173 DASAVLYTTVKSACASVALLHQKEIKGGTVWARQ--LGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPH  250 (676)
Q Consensus       173 g~afV~F~~~~~A~~A~~~l~~~~~~~~~i~v~~--~~~~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~  250 (676)
                      ++|+.+|..++.+..+...+... ..|.......  ..........++|||+|||+++++++|+++|+.|| |.+|.|+.
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~   79 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEI   79 (139)
T ss_dssp             --------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCC
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCCCcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEE
Confidence            45777787777777776654332 2222111100  01112344568999999999999999999999999 67999999


Q ss_pred             cCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCC
Q 005812          251 NTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKN  297 (676)
Q Consensus       251 ~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~  297 (676)
                      ++. ++++|||||+|.+.++|++|| .+|+..|.|+.|.|.++.+..
T Consensus        80 d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~  124 (139)
T 2hgn_A           80 GPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTG  124 (139)
T ss_dssp             SSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSC
T ss_pred             CCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCC
Confidence            975 999999999999999999999 689999999999999987654

>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

Probab=99.54  E-value=2.7e-15  Score=119.78  Aligned_cols=75  Identities=19%  Similarity=0.387  Sum_probs=71.6

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       218 ~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      +|||+|||+++++++|+++|++||.|.+|.++.++.++.++|||||+|.+.++|.+|++. ++..+.|+.|.|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            589999999999999999999999999999999988999999999999999999999995 999999999999875

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

Probab=99.54  E-value=1.1e-14  Score=123.61  Aligned_cols=78  Identities=21%  Similarity=0.363  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||.++++++|+++|+.||.|.+|.+.+      ++|||||+|.+.++|.+|+..|||..+.|+.|+|.|
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   97 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW   97 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCB
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEe
Confidence            34568999999999999999999999999999999984      679999999999999999999999999999999999


Q ss_pred             ecCC
Q 005812          293 AVPK  296 (676)
Q Consensus       293 a~~~  296 (676)
                      +.++
T Consensus        98 a~~~  101 (101)
T 2la4_A           98 GKER  101 (101)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8763

>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

Probab=99.54  E-value=1e-14  Score=142.85  Aligned_cols=84  Identities=13%  Similarity=0.205  Sum_probs=78.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCC--ceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFG--EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G--~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..++|||+|||+.+|+++|+++|+.||  .|..|+|++++.+++++|||||+|.+.++|.+||..||     +..|.|+.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~ln-----g~~~~Gr~  141 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLP-----KRELHGQN  141 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTST-----TSCBTTBC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcC-----CCeECCEE
Confidence            457999999999999999999999999  99999999999999999999999999999999999999     99999999


Q ss_pred             EEEEEccCchh
Q 005812          502 LTVLKALDKKL  512 (676)
Q Consensus       502 l~v~~a~~k~~  512 (676)
                      |.|.+|.+...
T Consensus       142 l~V~~a~~~~~  152 (229)
T 3q2s_C          142 PVVTPVNKQFL  152 (229)
T ss_dssp             CEEEECCHHHH
T ss_pred             eEEEECCCCcc
Confidence            99999986543

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

Probab=99.53  E-value=7e-14  Score=116.39  Aligned_cols=79  Identities=24%  Similarity=0.317  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||.++++++|+++|++||.|..|.+++        +||||+|.+.++|.+|+..||+..|.|+.|.|.
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            456678999999999999999999999999999999975        399999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus        78 ~a~~~~~   84 (92)
T 2dgt_A           78 LSTSRLR   84 (92)
T ss_dssp             ESSCCCS
T ss_pred             EccCCCC
Confidence            9987653

>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

Probab=99.53  E-value=2.8e-14  Score=122.92  Aligned_cols=80  Identities=20%  Similarity=0.369  Sum_probs=74.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||..+++++|+.+|+.||.|..|.|+.+      +|||||+|.+.++|.+|+..|+|..|.|+.|.|.|
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            446789999999999999999999999999999999874      68999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 005812          293 AVPKNI  298 (676)
Q Consensus       293 a~~~~~  298 (676)
                      +.++..
T Consensus        96 a~~~~~  101 (109)
T 1x4g_A           96 GKESPD  101 (109)
T ss_dssp             CCCCCS
T ss_pred             cCCCCC
Confidence            987653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.29  E-value=6.3e-16  Score=134.97  Aligned_cols=84  Identities=24%  Similarity=0.264  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCC
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS--------FVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLG  494 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~--------v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g  494 (676)
                      .+.++|||+|||+.+++++|+++|++||.|..        |.|+.++.++.++|||||+|.+.++|.+|+..||     +
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~-----g   79 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD-----G   79 (116)
Confidence            34689999999999999999999999999998        8899988889999999999999999999999999     9


Q ss_pred             eeecCcEEEEEEccCch
Q 005812          495 IFLKGRQLTVLKALDKK  511 (676)
Q Consensus       495 ~~l~gr~l~v~~a~~k~  511 (676)
                      ..|.|++|.|.++.++.
T Consensus        80 ~~~~g~~l~V~~a~~~~   96 (116)
T 2lcw_A           80 KEFSGNPIKVSFATRRA   96 (116)
Confidence            99999999999998764

>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}

Probab=99.53  E-value=6e-15  Score=126.58  Aligned_cols=83  Identities=16%  Similarity=0.299  Sum_probs=77.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCc---eEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGL---VWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPI  288 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~---i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i  288 (676)
                      .....++|||+|||+++++++|+++|+.||.   |..|.|+.++. |+++|||||+|.+.++|++|+. +++..++|+.|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            4456789999999999999999999999998   89999999986 9999999999999999999999 89999999999


Q ss_pred             EEEEecCC
Q 005812          289 AVDWAVPK  296 (676)
Q Consensus       289 ~v~~a~~~  296 (676)
                      .|.++.++
T Consensus        85 ~V~~a~~~   92 (107)
T 2lmi_A           85 EVYEINNE   92 (107)
T ss_dssp             CCEECCHH
T ss_pred             EEEECCHH
Confidence            99998764

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.53  E-value=1.6e-14  Score=121.30  Aligned_cols=79  Identities=22%  Similarity=0.393  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .+.++|||+|||+.+++++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|+..|+     +..|+|+.|
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l   83 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQ-----GAEIDGRSV   83 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTT-----EEEETTEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhC-----CCEECCeEE
Confidence            356899999999999999999999999988766     2467889999999999999999999999     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        84 ~v~~a~~~~   92 (96)
T 1fjc_A           84 SLYYTGEKG   92 (96)
T ss_dssp             EEEECSSSC
T ss_pred             EEEEcCCCC
Confidence            999998764

>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

Probab=99.53  E-value=3e-14  Score=121.33  Aligned_cols=75  Identities=23%  Similarity=0.387  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      +.++|||+|||+.+++++|+++|++||.|..|.++        ++||||+|.+.++|.+|+..||     +..|.|+.|.
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l~   76 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMN-----GKDLEGENIE   76 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHT-----TEEETTEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHC-----CCccCCCEEE
Confidence            45899999999999999999999999999999875        5699999999999999999999     9999999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.++.++.
T Consensus        77 v~~a~~~~   84 (103)
T 2dgu_A           77 IVFAKPPD   84 (103)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCc
Confidence            99998765

>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

Probab=99.53  E-value=1.8e-14  Score=124.44  Aligned_cols=76  Identities=26%  Similarity=0.404  Sum_probs=71.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++|||+|||+.+++++|+++|++||.|..|.|+.      ++|||||+|.+.++|++|++.|||..|.|+.|.|.|+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            467999999999999999999999999999999875      66899999999999999999999999999999999996


Q ss_pred             CC
Q 005812          295 PK  296 (676)
Q Consensus       295 ~~  296 (676)
                      ..
T Consensus        83 ~~   84 (111)
T 1whx_A           83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

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

Probab=99.53  E-value=2.9e-14  Score=118.21  Aligned_cols=77  Identities=22%  Similarity=0.312  Sum_probs=70.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++        ++||||+|.+.++|.+|+..||     +..|+|+.
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~~~~a~~A~~~l~-----g~~~~g~~   72 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLN-----GKEVKGKR   72 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHT-----TCEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhC-----CCEECCcE
Confidence            3456899999999999999999999999999999886        3499999999999999999999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        73 l~v~~a~~~~   82 (90)
T 2dnp_A           73 INVELSTKGQ   82 (90)
T ss_dssp             CEEEESCCCC
T ss_pred             EEEEECCCCC
Confidence            9999988753

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=2.1e-14  Score=120.83  Aligned_cols=80  Identities=19%  Similarity=0.316  Sum_probs=72.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||+.+++++|+++|+.||.|. +.++.+    .++|||||+|.+.++|.+|++.|||..|.|+.|.|.+
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34578999999999999999999999999997 666653    4789999999999999999999999999999999999


Q ss_pred             ecCCC
Q 005812          293 AVPKN  297 (676)
Q Consensus       293 a~~~~  297 (676)
                      +.++.
T Consensus        91 a~~~~   95 (97)
T 2e5j_A           91 ARQQR   95 (97)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98764

>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

Probab=99.52  E-value=7.9e-15  Score=128.53  Aligned_cols=80  Identities=24%  Similarity=0.348  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCcee--EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVV--SFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~--~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...++|||+|||+++|+++|+++|+.| .|.  .|+|+.++. |+++|||||+|.+.++|.+|+.. +     +..|+||
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~-----~~~l~gR  111 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-H-----KERIGHR  111 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-T-----TCCBTTB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-C-----CCEECCE
Confidence            345799999999999999999999999 566  899998876 99999999999999999999974 7     7999999


Q ss_pred             EEEEEEccCc
Q 005812          501 QLTVLKALDK  510 (676)
Q Consensus       501 ~l~v~~a~~k  510 (676)
                      .|.|.++.++
T Consensus       112 ~I~V~~a~~~  121 (126)
T 2hgm_A          112 YIEVFKSSQE  121 (126)
T ss_dssp             CCCCEEECHH
T ss_pred             EEEEEECCHH
Confidence            9999998654

>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

Probab=99.52  E-value=5.3e-14  Score=119.80  Aligned_cols=79  Identities=22%  Similarity=0.350  Sum_probs=72.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+++++++|+++|+.||.|..|.+++        +||||+|.+.++|.+|++.|++..|.|+.|.|.
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   78 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIV   78 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEE
Confidence            445678999999999999999999999999999999874        589999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus        79 ~a~~~~~   85 (103)
T 2dgu_A           79 FAKPPDQ   85 (103)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCcc
Confidence            9987654

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=7.3e-15  Score=127.97  Aligned_cols=86  Identities=20%  Similarity=0.244  Sum_probs=73.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||..+++++|+++|+.||.|..+.+..+..++.++|||||+|.+.++|.+|++.|+|..|.|+.|.|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            44678999999999999999999999999984332222222677999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 005812          293 AVPKNI  298 (676)
Q Consensus       293 a~~~~~  298 (676)
                      +.++..
T Consensus       102 a~~~~~  107 (115)
T 2cpx_A          102 GKNKKQ  107 (115)
T ss_dssp             CCCCSC
T ss_pred             ccCCCC
Confidence            987653

>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

Probab=99.52  E-value=5.4e-14  Score=118.19  Aligned_cols=77  Identities=19%  Similarity=0.384  Sum_probs=71.2

Q ss_pred             CCCCCcEEEEcCCCC-CCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          212 SKTQKWKLIIRNIPF-KAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~-~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      .....++|||+|||. ++++++|+++|+.||.|..|.+.        +|||||+|.+.++|.+|+..|+|..+.|+.|.|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            455789999999998 99999999999999999999983        589999999999999999999999999999999


Q ss_pred             EEecCC
Q 005812          291 DWAVPK  296 (676)
Q Consensus       291 ~~a~~~  296 (676)
                      .|+.++
T Consensus        90 ~~a~~~   95 (97)
T 2xnq_A           90 EVSSSN   95 (97)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            998764

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.52  E-value=5.6e-15  Score=134.10  Aligned_cols=85  Identities=22%  Similarity=0.308  Sum_probs=73.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEE--E---eecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCee
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFV--P---VLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIF  496 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~--i---~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~  496 (676)
                      ..++++|||+|||+.+++++|+++|+.||.|..+.  +   +....++.++|||||+|.+.++|.+|+..||     |..
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~ln-----g~~  116 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEAN-----GYV  116 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHT-----TBE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhC-----CCE
Confidence            44568999999999999999999999999987641  1   1112368899999999999999999999999     999


Q ss_pred             ecCcEEEEEEccCch
Q 005812          497 LKGRQLTVLKALDKK  511 (676)
Q Consensus       497 l~gr~l~v~~a~~k~  511 (676)
                      |.|+.|.|.+|.+..
T Consensus       117 ~~g~~l~V~~a~~~~  131 (143)
T 3egn_A          117 LFGKPMVVQFARSAR  131 (143)
T ss_dssp             ETTEECEEEECCCSC
T ss_pred             eCCcEEEEEECCCCC
Confidence            999999999998754

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

Probab=99.52  E-value=3.4e-14  Score=121.92  Aligned_cols=78  Identities=28%  Similarity=0.569  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||.++++++|+++|++||.|..|.++        +|||||+|.+.++|.+|+..|||..+.|+.|.|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            45667899999999999999999999999999999987        5899999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.++.
T Consensus        99 ~a~~~~  104 (108)
T 2jvo_A           99 YSKLPA  104 (108)
T ss_dssp             SCSCCC
T ss_pred             EecCCC
Confidence            997754

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

Probab=99.52  E-value=5.8e-14  Score=116.33  Aligned_cols=78  Identities=24%  Similarity=0.479  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+++++++|+++|++||.|..|.+++        +||||+|.+.++|++|++.|||..+.|+.|.|.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            455678999999999999999999999999999999975        389999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.+..
T Consensus        77 ~a~~~~   82 (90)
T 2dnp_A           77 LSTKGQ   82 (90)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            997764

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.52  E-value=2.7e-14  Score=122.07  Aligned_cols=80  Identities=20%  Similarity=0.355  Sum_probs=72.5

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCC----HHH----HHHHHH--HcCCCC
Q 005812          426 NTIFICNL----PFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKT----VEA----ATAAVS--ASKTTS  491 (676)
Q Consensus       426 ~~l~V~nL----p~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t----~~~----A~~Al~--~l~~~~  491 (676)
                      ..|||+||    |+.+++++|+++|+.||.|.+|.++.|+.+|+++|||||+|.+    +++    |.+|+.  .++   
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~ln---   79 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESS---   79 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTT---
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhc---
Confidence            58999999    9999999999999999999999999999999999999999996    333    889988  789   


Q ss_pred             CCCeeecCcEEEEEEccCc
Q 005812          492 GLGIFLKGRQLTVLKALDK  510 (676)
Q Consensus       492 ~~g~~l~gr~l~v~~a~~k  510 (676)
                        |..|+||+|.|.+-...
T Consensus        80 --g~~I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           80 --GCFIMGFKFEVILNKHS   96 (136)
T ss_dssp             --CEEETTEEEEEEECCTT
T ss_pred             --CCeecCcEEEEEECccc
Confidence              99999999999986553

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.52  E-value=2.6e-15  Score=127.54  Aligned_cols=83  Identities=23%  Similarity=0.310  Sum_probs=76.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||+++++++|+++|+.||.|.. .++.+..++.++|||||+|.+.++|.+|++ |||..|.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            346789999999999999999999999999988 667777788899999999999999999999 999999999999999


Q ss_pred             ecCCC
Q 005812          293 AVPKN  297 (676)
Q Consensus       293 a~~~~  297 (676)
                      +.++.
T Consensus        92 a~~~~   96 (101)
T 1fj7_A           92 PKGRD   96 (101)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            98764

>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

Probab=99.52  E-value=1.5e-14  Score=141.66  Aligned_cols=82  Identities=16%  Similarity=0.257  Sum_probs=77.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCC--ceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVG--LVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G--~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ..++|||+|||+.+++++|+++|+.||  .|.+|.|++++.+++++|||||+|.+.++|.+||+.||+..|.|+.|.|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ecCC
Q 005812          293 AVPK  296 (676)
Q Consensus       293 a~~~  296 (676)
                      +.+.
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8754

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

Probab=99.51  E-value=3.1e-14  Score=133.60  Aligned_cols=85  Identities=21%  Similarity=0.365  Sum_probs=79.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...++++|||+|||+.+++++|+++|+.||.|..|.|+.+. ++.++|||||+|.+.++|.+|+..||     +..|+|+
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~ln-----g~~l~Gr  157 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYK-----GVPLDGR  157 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHST-----TCBCSSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhC-----CCEECCE
Confidence            34557899999999999999999999999999999999887 89999999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      .|.|.+|....
T Consensus       158 ~l~V~~a~~~~  168 (177)
T 2f3j_A          158 PMDIQLVASQI  168 (177)
T ss_dssp             BCEEEEESSGG
T ss_pred             EEEEEEecCCC
Confidence            99999987653

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

Probab=99.51  E-value=2.6e-14  Score=120.05  Aligned_cols=79  Identities=19%  Similarity=0.167  Sum_probs=71.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEE-EeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFV-PVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~-i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      ..++|||+|||+.+++++|+++|+.||.|..|+ ++.+..    .|.|||+|.+.++|.+|+..||     |..|+|++|
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~----~~~afV~f~~~~~a~~Ai~~l~-----g~~~~g~~l   84 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE----TAVVNVTYSSKDQARQALDKLN-----GFQLENFTL   84 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS----SEEEEEEESSHHHHHHHHHHHT-----TCBCSSCBC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC----CCEEEEEECCHHHHHHHHHHhC-----CCEECCcEE
Confidence            357999999999999999999999999999994 776654    3449999999999999999999     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.+++
T Consensus        85 ~V~~a~~~~   93 (96)
T 2e44_A           85 KVAYIPDEM   93 (96)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEcCccc
Confidence            999998874

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.51  E-value=4.1e-15  Score=132.96  Aligned_cols=81  Identities=17%  Similarity=0.235  Sum_probs=74.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      ...++|||+|||+++|+++|+++|++|| |..|.|++++. ++++|||||+|.+.++|.+|+ .+|     +..|+||.|
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~-----g~~l~gR~i  115 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKD-----RANMQHRYI  115 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCC-----SCSSSSCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhC-----CCEECCEEE
Confidence            3457999999999999999999999999 67999999875 999999999999999999999 889     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.+++
T Consensus       116 ~V~~a~~~~  124 (139)
T 2hgn_A          116 ELFLNSTTG  124 (139)
T ss_dssp             CCEECCCSC
T ss_pred             EEEECCCCC
Confidence            999987654

>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

Probab=99.51  E-value=1.7e-14  Score=124.53  Aligned_cols=75  Identities=20%  Similarity=0.095  Sum_probs=69.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|++||.|..|.++.      ++|||||+|.+.++|.+|+..||     |..|+|++|.|
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~-----g~~~~g~~l~V   78 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLA-----YSKFHHVPLYL   78 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHT-----TCBSSSSBCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhC-----CCEECCeEEEE
Confidence            57999999999999999999999999999997753      57899999999999999999999     99999999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      .|+...
T Consensus        79 ~~a~~~   84 (111)
T 1whx_A           79 EWAPIG   84 (111)
T ss_dssp             EEEETT
T ss_pred             EECCCC
Confidence            998764

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.51  E-value=2.5e-14  Score=120.13  Aligned_cols=81  Identities=23%  Similarity=0.445  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|+..|+|..|.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999988765     2367899999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      ++.++.
T Consensus        87 ~a~~~~   92 (96)
T 1fjc_A           87 YTGEKG   92 (96)
T ss_dssp             ECSSSC
T ss_pred             EcCCCC
Confidence            997754

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.51  E-value=7.1e-14  Score=122.26  Aligned_cols=80  Identities=16%  Similarity=0.365  Sum_probs=72.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeE-EEEEecCHHHHHHHHHHhCCceeCC--eeEEE
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGF-AFVKFTCKRDAESAIQKFNGQKFGK--RPIAV  290 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~-afV~f~~~~~A~~A~~~l~~~~~~g--~~i~v  290 (676)
                      ..--.|||+||++.+|+++|+++|++||.|.+|+++.+     .+|| |||+|.+.++|..|++.|||..|.|  +.|+|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            34467889999999999999999999999999998864     3577 9999999999999999999999987  99999


Q ss_pred             EEecCCCC
Q 005812          291 DWAVPKNI  298 (676)
Q Consensus       291 ~~a~~~~~  298 (676)
                      +|+++...
T Consensus       101 ~~ak~~~l  108 (130)
T 3zzy_A          101 DFSKLTSL  108 (130)
T ss_dssp             EECSCSSC
T ss_pred             EecCCCce
Confidence            99988754

>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

Probab=99.51  E-value=5.6e-14  Score=121.25  Aligned_cols=75  Identities=28%  Similarity=0.445  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          423 ELQNTIFICNLPFD-LDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       423 ~~~~~l~V~nLp~~-~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+++|||+|||+. +++++|+++|++||.|..|.+        ++|||||+|.+.++|.+|+..|+     +..|+|+.
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~~   91 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGEN-----GRVLAGQT   91 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHT-----TCEETTEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcC-----CCEECCeE
Confidence            34589999999999 999999999999999999987        47999999999999999999999     99999999


Q ss_pred             EEEEEccCc
Q 005812          502 LTVLKALDK  510 (676)
Q Consensus       502 l~v~~a~~k  510 (676)
                      |.|.++.++
T Consensus        92 l~V~~a~~~  100 (110)
T 1wf1_A           92 LDINMAGEP  100 (110)
T ss_dssp             CCEEESCCC
T ss_pred             EEEEECCCC
Confidence            999998754

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.26  E-value=1.4e-15  Score=132.76  Aligned_cols=86  Identities=23%  Similarity=0.443  Sum_probs=80.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEE--------EEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWN--------VYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG  284 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~--------v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~  284 (676)
                      ....++|||+|||..+++++|+++|+.||.|..        |.|+.++.++.++|||||+|.+.++|.+|+..|||..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            345689999999999999999999999999998        899999888999999999999999999999999999999


Q ss_pred             CeeEEEEEecCCCC
Q 005812          285 KRPIAVDWAVPKNI  298 (676)
Q Consensus       285 g~~i~v~~a~~~~~  298 (676)
                      |+.|.|.|+.++..
T Consensus        84 g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           84 GNPIKVSFATRRAD   97 (116)
Confidence            99999999987654

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

Probab=99.51  E-value=2.1e-14  Score=120.53  Aligned_cols=77  Identities=19%  Similarity=0.391  Sum_probs=70.2

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          422 DELQNTIFICNLPF-DLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       422 ~~~~~~l~V~nLp~-~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ..+.++|||+|||+ .+++++|+++|++||.|..|.+.        +|||||+|.+.++|.+|+..||     +..+.|+
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~-----g~~~~g~   73 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECES-----QEMNFGK   73 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHT-----CSSCBTT
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcC-----CCeeCCc
Confidence            34568999999998 99999999999999999999873        7899999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      +|.|.++.++.
T Consensus        74 ~l~V~~a~~~~   84 (96)
T 2kvi_A           74 KLILEVSSSNA   84 (96)
T ss_dssp             TBCEEEEECCC
T ss_pred             EEEEEEcCcCC
Confidence            99999997754

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=2.3e-14  Score=119.58  Aligned_cols=76  Identities=22%  Similarity=0.328  Sum_probs=68.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCc-eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCC-eeecCcE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGE-VVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLG-IFLKGRQ  501 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~-v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g-~~l~gr~  501 (676)
                      ..++|||+|||+.+++++|+++|++||. |..+.+.       ++|||||+|.+.++|.+|+..||     + ..|+|+.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~-----g~~~~~g~~   74 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLS-----GKVELHGKI   74 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHT-----TTCEETTEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHcc-----CCeeECCEE
Confidence            4579999999999999999999999999 6665442       47899999999999999999999     9 9999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        75 l~v~~a~~~~   84 (93)
T 2cqh_A           75 MEVDYSVSKK   84 (93)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEccCcc
Confidence            9999998764

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.50  E-value=2.9e-14  Score=121.89  Aligned_cols=78  Identities=15%  Similarity=0.146  Sum_probs=71.4

Q ss_pred             cEEEEcCC----CCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecC----HHH----HHHHHH--HhCCce
Q 005812          217 WKLIIRNI----PFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC----KRD----AESAIQ--KFNGQK  282 (676)
Q Consensus       217 ~~v~V~nL----p~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~----~~~----A~~A~~--~l~~~~  282 (676)
                      ..|||+||    |+.+++.+|+++|+.||.|.+|.++.|+.||.++|||||+|.+    +++    |.+|+.  .|+|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            58999999    9999999999999999999999999999999999999999996    433    888988  789999


Q ss_pred             eCCeeEEEEEec
Q 005812          283 FGKRPIAVDWAV  294 (676)
Q Consensus       283 ~~g~~i~v~~a~  294 (676)
                      |.|+.|+|.+-.
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999863

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.50  E-value=1.6e-14  Score=122.79  Aligned_cols=82  Identities=24%  Similarity=0.384  Sum_probs=76.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ...++|||+|||+++++++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|++|+.  ++..+.|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            356899999999999999999999999999999999998 89999999999999999999999  999999999999999


Q ss_pred             cCCCC
Q 005812          294 VPKNI  298 (676)
Q Consensus       294 ~~~~~  298 (676)
                      .++..
T Consensus        84 ~~~~~   88 (102)
T 2xs2_A           84 IRKQN   88 (102)
T ss_dssp             EECC-
T ss_pred             CcCcc
Confidence            76643

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=4.3e-14  Score=117.92  Aligned_cols=80  Identities=23%  Similarity=0.391  Sum_probs=71.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCc-eEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCC-ceeCCeeEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGL-VWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG-QKFGKRPIA  289 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~-i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~-~~~~g~~i~  289 (676)
                      .....++|||+|||.++++++|+++|++||. |..+.+.       ++|||||+|.+.++|.+|++.||| ..+.|+.|+
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~   76 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIME   76 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEE
Confidence            3456789999999999999999999999999 6655552       579999999999999999999999 999999999


Q ss_pred             EEEecCCCC
Q 005812          290 VDWAVPKNI  298 (676)
Q Consensus       290 v~~a~~~~~  298 (676)
                      |.|+.++..
T Consensus        77 v~~a~~~~~   85 (93)
T 2cqh_A           77 VDYSVSKKL   85 (93)
T ss_dssp             EEECCCCCC
T ss_pred             EEEccCccc
Confidence            999987643

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=5.2e-14  Score=120.23  Aligned_cols=81  Identities=15%  Similarity=0.306  Sum_probs=72.0

Q ss_pred             CCCCCcEEEE--cCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee-----C
Q 005812          212 SKTQKWKLII--RNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF-----G  284 (676)
Q Consensus       212 ~~~~~~~v~V--~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~-----~  284 (676)
                      ...+.++|||  +||++++++++|+++|++||.|.+|.|+.      .+|||||+|.+.++|++|++.|||..+     .
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~   94 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   94 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCC
Confidence            3445688999  67999999999999999999999998875      368999999999999999999999988     6


Q ss_pred             CeeEEEEEecCCCC
Q 005812          285 KRPIAVDWAVPKNI  298 (676)
Q Consensus       285 g~~i~v~~a~~~~~  298 (676)
                      |++|.|.|+....+
T Consensus        95 g~~l~v~~a~~~p~  108 (114)
T 2cq2_A           95 KITLYLNFVEKVQW  108 (114)
T ss_dssp             EEECEEEEESCCCC
T ss_pred             CcEEEEEecccCcc
Confidence            89999999976544

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

Probab=99.50  E-value=4.5e-14  Score=118.52  Aligned_cols=78  Identities=19%  Similarity=0.367  Sum_probs=70.8

Q ss_pred             CCCCCcEEEEcCCCC-CCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          212 SKTQKWKLIIRNIPF-KAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~-~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      ...+.++|||+|||+ .+++++|+++|++||.|..|.+.        +|||||+|.+.++|..|+..|+|..+.|+.|.|
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            345678999999998 99999999999999999999984        589999999999999999999999999999999


Q ss_pred             EEecCCC
Q 005812          291 DWAVPKN  297 (676)
Q Consensus       291 ~~a~~~~  297 (676)
                      .|+.++.
T Consensus        78 ~~a~~~~   84 (96)
T 2kvi_A           78 EVSSSNA   84 (96)
T ss_dssp             EEEECCC
T ss_pred             EEcCcCC
Confidence            9997754

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=2.1e-14  Score=125.52  Aligned_cols=81  Identities=25%  Similarity=0.396  Sum_probs=74.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCce----EEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEE
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLV----WNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIA  289 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i----~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~  289 (676)
                      ....+|||+|||+++++++|+++|+.||.|    ..|.|+.+. +|+++|||||+|.+.++|++|++. |+..|.|+.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            356799999999999999999999999975    689999884 899999999999999999999996 99999999999


Q ss_pred             EEEecCC
Q 005812          290 VDWAVPK  296 (676)
Q Consensus       290 v~~a~~~  296 (676)
                      |..+.++
T Consensus        99 V~~a~~~  105 (123)
T 2dha_A           99 LFRSTAA  105 (123)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9988654

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

Probab=99.49  E-value=1.6e-13  Score=115.90  Aligned_cols=78  Identities=28%  Similarity=0.443  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccC--CceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPV--GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIA  289 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~  289 (676)
                      .....++|||+|||+.+++++|+++|+.|  |.|..|.++        +|||||+|.+.++|.+|+..|||..|.|+.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIE   82 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            44567899999999999999999999999  999998875        47999999999999999999999999999999


Q ss_pred             EEEecCCC
Q 005812          290 VDWAVPKN  297 (676)
Q Consensus       290 v~~a~~~~  297 (676)
                      |.|+.++.
T Consensus        83 v~~a~~~~   90 (99)
T 2cpd_A           83 VTLAKPVD   90 (99)
T ss_dssp             EECCCCCC
T ss_pred             EEECCCCC
Confidence            99998764

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

Probab=99.49  E-value=3.8e-14  Score=114.47  Aligned_cols=74  Identities=20%  Similarity=0.282  Sum_probs=65.8

Q ss_pred             CCCe-EEEcCCCCCCCHHH----HHHHHHhC-CceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee
Q 005812          424 LQNT-IFICNLPFDLDNEE----VKQRFSAF-GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL  497 (676)
Q Consensus       424 ~~~~-l~V~nLp~~~teed----l~~~F~~~-G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l  497 (676)
                      +..+ |||+|||+.+++++    |+++|++| |.|..|       ++   |+|||.|.+.++|.+|++.|+     |..|
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~-----G~~l   71 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRME-----NEDV   71 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHT-----TCCS
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhc-----CCcc
Confidence            3455 99999999999988    55899999 599997       23   999999999999999999999     9999


Q ss_pred             cCcEEEEEEccCchh
Q 005812          498 KGRQLTVLKALDKKL  512 (676)
Q Consensus       498 ~gr~l~v~~a~~k~~  512 (676)
                      .||+|+|.+|..+..
T Consensus        72 ~gr~i~v~~A~~~sd   86 (96)
T 2diu_A           72 FGNRIIVSFTPKNRE   86 (96)
T ss_dssp             SSSCCEEESSCCSCC
T ss_pred             CCceEEEEecCCCcc
Confidence            999999999987653

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=3.9e-14  Score=121.02  Aligned_cols=79  Identities=13%  Similarity=0.114  Sum_probs=69.9

Q ss_pred             CCCCCeEEE--cCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee--
Q 005812          422 DELQNTIFI--CNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL--  497 (676)
Q Consensus       422 ~~~~~~l~V--~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l--  497 (676)
                      ..++++|||  +|||+.+++++|+++|++||.|..|.++.      .+|||||+|.+.++|.+|+..||     |..|  
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~ln-----G~~~~~   90 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLN-----GKEVVD   90 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTT-----TCEEEC
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhC-----CCEEcc
Confidence            345689999  66999999999999999999999987652      37899999999999999999999     9988  


Q ss_pred             ---cCcEEEEEEccCch
Q 005812          498 ---KGRQLTVLKALDKK  511 (676)
Q Consensus       498 ---~gr~l~v~~a~~k~  511 (676)
                         .|++|.|.++...+
T Consensus        91 ~lg~g~~l~v~~a~~~p  107 (114)
T 2cq2_A           91 DLGQKITLYLNFVEKVQ  107 (114)
T ss_dssp             TTSCEEECEEEEESCCC
T ss_pred             ccCCCcEEEEEecccCc
Confidence               79999999987643

>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}

Probab=99.49  E-value=7.4e-14  Score=115.22  Aligned_cols=78  Identities=22%  Similarity=0.316  Sum_probs=63.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|+|+.+     ++|||||+|.+.++|.+    ++..   .+.+.|+.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~---~~~~~g~~   75 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGE---DLIIKGIS   75 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTC---EEEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCC---CcccCCEE
Confidence            345689999999999999999999999999999988764     68999999999999984    4411   35567999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.+|.++.
T Consensus        76 v~v~~a~~k~   85 (89)
T 3d2w_A           76 VHISNAEPKH   85 (89)
T ss_dssp             EEEEECC---
T ss_pred             EEEEEcCCCC
Confidence            9999998764

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

Probab=99.49  E-value=6.7e-14  Score=131.29  Aligned_cols=85  Identities=22%  Similarity=0.399  Sum_probs=79.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|+.||.|..|.|+.+. ++.++|||||+|.+.++|.+|++.|+|..|.|+.|.|.
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999988 89999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.+..
T Consensus       163 ~a~~~~  168 (177)
T 2f3j_A          163 LVASQI  168 (177)
T ss_dssp             EESSGG
T ss_pred             EecCCC
Confidence            997653

>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

Probab=99.49  E-value=3.9e-14  Score=124.11  Aligned_cols=82  Identities=27%  Similarity=0.419  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceE--EEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVW--NVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIA  289 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~  289 (676)
                      .....++|||+|||+.+++++|+++|+.| .|.  +|+|+.++. |+++|||||+|.+.++|++|++. ++..|.|+.|.
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~  114 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEE
Confidence            34457899999999999999999999999 566  899999986 99999999999999999999995 88999999999


Q ss_pred             EEEecCC
Q 005812          290 VDWAVPK  296 (676)
Q Consensus       290 v~~a~~~  296 (676)
                      |.++.++
T Consensus       115 V~~a~~~  121 (126)
T 2hgm_A          115 VFKSSQE  121 (126)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9988654

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

Probab=99.49  E-value=1.6e-13  Score=116.65  Aligned_cols=82  Identities=21%  Similarity=0.164  Sum_probs=72.8

Q ss_pred             CCCCeEEEcCCCC-----CCCHHHHHHHHHhCCceeEEEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHcCCCCCCCee
Q 005812          423 ELQNTIFICNLPF-----DLDNEEVKQRFSAFGEVVSFVPVLHQVT-KRPKGTGFLKFKTVEAATAAVSASKTTSGLGIF  496 (676)
Q Consensus       423 ~~~~~l~V~nLp~-----~~teedl~~~F~~~G~v~~v~i~~~~~~-~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~  496 (676)
                      .++++|+|+||..     +-++++|+++|++||.|.+|.|+.++.+ +.++|||||+|.+.++|.+|+..||     |..
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~ln-----G~~   80 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLN-----GRY   80 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHT-----TCE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHC-----CCE
Confidence            3568999999963     2378999999999999999999988653 6789999999999999999999999     999


Q ss_pred             ecCcEEEEEEccC
Q 005812          497 LKGRQLTVLKALD  509 (676)
Q Consensus       497 l~gr~l~v~~a~~  509 (676)
                      |+||.|.|.++..
T Consensus        81 ~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           81 FGGRVVKACFYNL   93 (105)
T ss_dssp             ETTEECEEEECCH
T ss_pred             ECCcEEEEEEcCH
Confidence            9999999999865

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.48  E-value=9.3e-14  Score=126.20  Aligned_cols=82  Identities=15%  Similarity=0.311  Sum_probs=73.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC--eeEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK--RPIAV  290 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g--~~i~v  290 (676)
                      .....+|||+||++.+++++|+++|++||.|.+|.|..+.    ++|||||+|.+.++|..|++.|||..|.|  +.|+|
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V  118 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  118 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEE
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEE
Confidence            3445679999999999999999999999999999997542    67999999999999999999999999965  99999


Q ss_pred             EEecCCCC
Q 005812          291 DWAVPKNI  298 (676)
Q Consensus       291 ~~a~~~~~  298 (676)
                      +|++++..
T Consensus       119 ~~Ak~~~l  126 (164)
T 1sjr_A          119 DFSKLTSL  126 (164)
T ss_dssp             EECSSSSC
T ss_pred             EEecCCcc
Confidence            99987643

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=2.6e-13  Score=114.15  Aligned_cols=76  Identities=24%  Similarity=0.420  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .+.++|||+||  .+++++|+++|++||.|..|.+.      .++|||||+|.+.++|.+|+..||     +..|.|++|
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~-----g~~~~g~~l   79 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELN-----GTQVESVQL   79 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTT-----TEEETTEEE
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhC-----CCeECCeEE
Confidence            35689999996  89999999999999999999873      468999999999999999999999     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        80 ~v~~a~~~~   88 (97)
T 1x5p_A           80 KVNIARKQP   88 (97)
T ss_dssp             EEECCSSCC
T ss_pred             EEEECCCCC
Confidence            999998764

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.48  E-value=7.2e-14  Score=115.21  Aligned_cols=74  Identities=23%  Similarity=0.299  Sum_probs=68.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|++| .|..+++.      .++|||||+|.+.++|.+|+..||     |..++|++|.|
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~-----g~~~~g~~l~V   72 (88)
T 1wg1_A            5 SSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFH-----QYSFRGKDLIV   72 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHT-----TEEETTEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhC-----CCeECCcEEEE
Confidence            4799999999999999999999999 99999874      468999999999999999999999     99999999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      .++...
T Consensus        73 ~~a~~~   78 (88)
T 1wg1_A           73 QLQPTD   78 (88)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            998653

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=1.3e-13  Score=115.19  Aligned_cols=79  Identities=18%  Similarity=0.271  Sum_probs=69.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||+++++++|+++|+.||.|.+|  +.++.++.   ||||+|.+.++|.+|+. |+|..|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~   78 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRP   78 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEE
Confidence            4456799999999999999999999999999987  44444554   99999999999999999 999999999999998


Q ss_pred             ecCCC
Q 005812          293 AVPKN  297 (676)
Q Consensus       293 a~~~~  297 (676)
                      +.++.
T Consensus        79 a~~~~   83 (94)
T 2e5g_A           79 REQKE   83 (94)
T ss_dssp             SCCSC
T ss_pred             CCcCC
Confidence            86654

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.48  E-value=8.2e-14  Score=114.86  Aligned_cols=76  Identities=21%  Similarity=0.347  Sum_probs=70.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++|||+|||+++++++|+++|++| .|.++.+.      +++|||||+|.+.++|.+|++.|||..+.|+.|+|.|+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            56789999999999999999999999 99999885      388999999999999999999999999999999999996


Q ss_pred             CCC
Q 005812          295 PKN  297 (676)
Q Consensus       295 ~~~  297 (676)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            543

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

Probab=99.48  E-value=7.6e-14  Score=117.17  Aligned_cols=81  Identities=22%  Similarity=0.358  Sum_probs=73.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEE-EEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNV-YIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      ....++|||+|||+.+++++|+++|+.||.|..| .++.++.+    |.|||+|.+.++|.+|+..|||..|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~----~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   87 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNGFQLENFTLKVA   87 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3456899999999999999999999999999999 58887643    349999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      ++.++.
T Consensus        88 ~a~~~~   93 (96)
T 2e44_A           88 YIPDEM   93 (96)
T ss_dssp             ECCCCC
T ss_pred             EcCccc
Confidence            998763

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=8.3e-14  Score=116.40  Aligned_cols=76  Identities=25%  Similarity=0.376  Sum_probs=68.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|+.||.|..|  +.+..++.   ||||+|.+.++|.+|+. |+     +..|+|+.|.|
T Consensus         8 ~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~-----g~~~~g~~l~V   76 (94)
T 2e5g_A            8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QS-----QHSLGGHRLRV   76 (94)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CS-----CCEETTEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cC-----CeEECCEEEEE
Confidence            4799999999999999999999999999987  55655554   99999999999999999 99     99999999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .++.++.
T Consensus        77 ~~a~~~~   83 (94)
T 2e5g_A           77 RPREQKE   83 (94)
T ss_dssp             BCSCCSC
T ss_pred             EECCcCC
Confidence            9887653

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=2.9e-13  Score=113.85  Aligned_cols=79  Identities=18%  Similarity=0.314  Sum_probs=71.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+||  ++++++|+++|++||.|..|.|..      ++|||||+|.+.++|.+|+..|+|..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~   82 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   82 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecC------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            3456789999996  899999999999999999999953      77999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      |+.++..
T Consensus        83 ~a~~~~~   89 (97)
T 1x5p_A           83 IARKQPM   89 (97)
T ss_dssp             CCSSCCC
T ss_pred             ECCCCCC
Confidence            9987653

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

Probab=99.48  E-value=1.6e-13  Score=110.86  Aligned_cols=75  Identities=19%  Similarity=0.261  Sum_probs=65.9

Q ss_pred             CCcEEEEcCCCCCCCHHH----HHHhhccC-CceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEE
Q 005812          215 QKWKLIIRNIPFKAKVNE----IKDMFSPV-GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIA  289 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~----l~~~F~~~-G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~  289 (676)
                      ..+.|||+|||+.+++++    |+++|++| |.|.+|       ++   |+|||.|.+.++|++|++.|+|..+.|++|+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            334499999999999988    55899999 599988       23   9999999999999999999999999999999


Q ss_pred             EEEecCCCCC
Q 005812          290 VDWAVPKNIY  299 (676)
Q Consensus       290 v~~a~~~~~~  299 (676)
                      |.+++.+.+.
T Consensus        78 v~~A~~~sd~   87 (96)
T 2diu_A           78 VSFTPKNREL   87 (96)
T ss_dssp             EESSCCSCCC
T ss_pred             EEecCCCcce
Confidence            9999876543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.48  E-value=1.9e-13  Score=119.58  Aligned_cols=76  Identities=18%  Similarity=0.202  Sum_probs=69.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHcCCCCCCCeeecC--cEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGT-GFLKFKTVEAATAAVSASKTTSGLGIFLKG--RQL  502 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~-afV~F~t~~~A~~Al~~l~~~~~~g~~l~g--r~l  502 (676)
                      ..|||+||++.+|+++|+++|++||.|.+|+++.+     .+|| |||+|.+.++|.+|++.||     |..|.|  +.|
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~Ln-----G~~i~g~~~~L   98 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLD-----GQNIYNACCTL   98 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHT-----TCEEETTEEEE
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcC-----CCeecCCCcEE
Confidence            57889999999999999999999999999987754     2677 9999999999999999999     999988  899


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      +|.|++++.
T Consensus        99 rI~~ak~~~  107 (130)
T 3zzy_A           99 RIDFSKLTS  107 (130)
T ss_dssp             EEEECSCSS
T ss_pred             EEEecCCCc
Confidence            999998753

>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

Probab=99.47  E-value=1.4e-13  Score=118.68  Aligned_cols=77  Identities=25%  Similarity=0.429  Sum_probs=70.9

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          213 KTQKWKLIIRNIPFK-AKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~-~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      ....++|||+|||+. +++++|+++|++||.|..|.+        ++|||||+|.+.++|.+|++.|++..|.|+.|.|.
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   95 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN   95 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            344589999999999 999999999999999999998        46899999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.+..
T Consensus        96 ~a~~~~  101 (110)
T 1wf1_A           96 MAGEPK  101 (110)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            997543

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.47  E-value=1.4e-13  Score=125.02  Aligned_cols=78  Identities=18%  Similarity=0.186  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC--cEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG--RQL  502 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g--r~l  502 (676)
                      ..+|||+|||+.+++++|+++|++||.|.+|+|+.+    .++|||||+|.+.++|.+|++.||     |..|.|  +.|
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~Ln-----G~~i~g~g~~L  116 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLD-----GQNIYNACCTL  116 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHST-----TBCSSSSCSCE
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhC-----CCEecCCCcEE
Confidence            357899999999999999999999999999988643    257999999999999999999999     999965  999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      +|.|++++.
T Consensus       117 ~V~~Ak~~~  125 (164)
T 1sjr_A          117 RIDFSKLTS  125 (164)
T ss_dssp             EEEECSSSS
T ss_pred             EEEEecCCc
Confidence            999998763

>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}

Probab=99.46  E-value=1.8e-13  Score=112.81  Aligned_cols=77  Identities=25%  Similarity=0.417  Sum_probs=63.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCce--eCCeeEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK--FGKRPIA  289 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~--~~g~~i~  289 (676)
                      .....++|||+|||+++++++|+++|++||.|.+|.|+++     ++|||||+|.+.++|++    +++..  +.|+.|.
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~   77 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVH   77 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEE
Confidence            3456789999999999999999999999999999999985     78999999999999983    45655  4699999


Q ss_pred             EEEecCCC
Q 005812          290 VDWAVPKN  297 (676)
Q Consensus       290 v~~a~~~~  297 (676)
                      |.++.++.
T Consensus        78 v~~a~~k~   85 (89)
T 3d2w_A           78 ISNAEPKH   85 (89)
T ss_dssp             EEECC---
T ss_pred             EEEcCCCC
Confidence            99998764

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.46  E-value=3.3e-14  Score=128.98  Aligned_cols=83  Identities=18%  Similarity=0.295  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEE--------EEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNV--------YIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF  283 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v--------~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  283 (676)
                      .....++|||+|||+.+++++|+.+|+.||.|..+        .+.   .+|.++|||||+|.+.++|.+|+..|||..|
T Consensus        41 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~---~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~  117 (143)
T 3egn_A           41 PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM---KEGRMKGQAFIGLPNEKAAAKALKEANGYVL  117 (143)
T ss_dssp             CCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE---EETTTEEEEEEECSSHHHHHHHHHHHTTBEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec---cCCCcccEEEEEeCCHHHHHHHHHHhCCCEe
Confidence            34567899999999999999999999999998764        333   3688999999999999999999999999999


Q ss_pred             CCeeEEEEEecCCC
Q 005812          284 GKRPIAVDWAVPKN  297 (676)
Q Consensus       284 ~g~~i~v~~a~~~~  297 (676)
                      .|+.|.|.|+.+..
T Consensus       118 ~g~~l~V~~a~~~~  131 (143)
T 3egn_A          118 FGKPMVVQFARSAR  131 (143)
T ss_dssp             TTEECEEEECCCSC
T ss_pred             CCcEEEEEECCCCC
Confidence            99999999997654

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.46  E-value=4.7e-13  Score=127.47  Aligned_cols=114  Identities=18%  Similarity=0.235  Sum_probs=91.2

Q ss_pred             CHHHHHHHHHHh--CCCeecCeEEEEecCCCCCCC---------CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEc
Q 005812          181 TVKSACASVALL--HQKEIKGGTVWARQLGGEGSK---------TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIP  249 (676)
Q Consensus       181 ~~~~A~~A~~~l--~~~~~~~~~i~v~~~~~~~~~---------~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~  249 (676)
                      +.+.+..|+...  ....+.+....++.....+.+         ...++|||+|||+.+++++|+++|++||.|..|+|+
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~  142 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR  142 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEE
Confidence            567888888876  444555555555544221111         124899999999999999999999999999999999


Q ss_pred             ccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          250 HNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       250 ~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      ++. ++.++|||||+|.+.++|.+|+..+ +..+.|+.|.|.|+...
T Consensus       143 ~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          143 RTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDY  187 (193)
T ss_dssp             ECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC
T ss_pred             ECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHH
Confidence            886 5889999999999999999999864 56999999999987543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.46  E-value=5.7e-13  Score=116.11  Aligned_cols=74  Identities=19%  Similarity=0.209  Sum_probs=66.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHcCCCCCCCeeecC--cEEE
Q 005812          427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGT-GFLKFKTVEAATAAVSASKTTSGLGIFLKG--RQLT  503 (676)
Q Consensus       427 ~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~-afV~F~t~~~A~~Al~~l~~~~~~g~~l~g--r~l~  503 (676)
                      .|||+|||+.+++++|+++|++||.|..|+|+..      .|| |||+|.+.++|..|+..||     |..|.|  +.|.
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~Ln-----G~~i~g~~~~l~   95 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALN-----GADIYAGCCTLK   95 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHT-----TCCCBTTBSEEE
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhC-----CCEecCCCeEEE
Confidence            4679999999999999999999999999988642      276 9999999999999999999     999987  6999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.+|.++.
T Consensus        96 V~~Ak~~~  103 (124)
T 2e5i_A           96 IEYARPTR  103 (124)
T ss_dssp             EECCSCSC
T ss_pred             EEEecCCc
Confidence            99998764

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.44  E-value=4.2e-13  Score=116.93  Aligned_cols=76  Identities=25%  Similarity=0.373  Sum_probs=68.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeE-EEEEecCHHHHHHHHHHhCCceeCC--eeEEEEEe
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGF-AFVKFTCKRDAESAIQKFNGQKFGK--RPIAVDWA  293 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~-afV~f~~~~~A~~A~~~l~~~~~~g--~~i~v~~a  293 (676)
                      ..|||+|||+.+++++|+++|++||.|.+|.|+..      .|| |||+|.+.++|..|++.|||..|.|  +.|+|.++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            45689999999999999999999999999999652      276 9999999999999999999999977  69999999


Q ss_pred             cCCCC
Q 005812          294 VPKNI  298 (676)
Q Consensus       294 ~~~~~  298 (676)
                      .++..
T Consensus       100 k~~~l  104 (124)
T 2e5i_A          100 RPTRL  104 (124)
T ss_dssp             SCSCC
T ss_pred             cCCcc
Confidence            88753

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

Probab=99.44  E-value=3.3e-13  Score=114.66  Aligned_cols=83  Identities=20%  Similarity=0.166  Sum_probs=73.5

Q ss_pred             CCCCcEEEEcCCCC-----CCCHHHHHHhhccCCceEEEEEcccCCC-CCceeEEEEEecCHHHHHHHHHHhCCceeCCe
Q 005812          213 KTQKWKLIIRNIPF-----KAKVNEIKDMFSPVGLVWNVYIPHNTDT-GLSKGFAFVKFTCKRDAESAIQKFNGQKFGKR  286 (676)
Q Consensus       213 ~~~~~~v~V~nLp~-----~~~e~~l~~~F~~~G~i~~v~i~~~~~~-~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  286 (676)
                      ..++++|+|+||..     +-++++|+++|++||.|.+|.|+.++.+ +.++|||||+|.+.++|.+|++.|||..|.|+
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            35678999999963     2368999999999999999999988654 67899999999999999999999999999999


Q ss_pred             eEEEEEecC
Q 005812          287 PIAVDWAVP  295 (676)
Q Consensus       287 ~i~v~~a~~  295 (676)
                      .|.|.++.+
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999865

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

Probab=99.44  E-value=1.6e-13  Score=119.09  Aligned_cols=78  Identities=24%  Similarity=0.367  Sum_probs=68.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVT---KRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~---~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ..++|||+|||+.+++++|+++|++||.|. +.++.+..+   |.++|||||+|.+.++|.+|++.|+       .++|+
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~-------~~~G~   78 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL-------EEDGK   78 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE-------EETTE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh-------hcCCc
Confidence            358999999999999999999999999999 878877766   7899999999999999999999986       47788


Q ss_pred             EEEEEEccC
Q 005812          501 QLTVLKALD  509 (676)
Q Consensus       501 ~l~v~~a~~  509 (676)
                      .|.+..+..
T Consensus        79 ~~~~~~~~~   87 (114)
T 2dnl_A           79 LYLCVSSPT   87 (114)
T ss_dssp             EEEEECCSS
T ss_pred             EEEeccCCC
Confidence            887766543

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

Probab=99.44  E-value=2.7e-13  Score=117.61  Aligned_cols=78  Identities=19%  Similarity=0.270  Sum_probs=66.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCC---CCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDT---GLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIA  289 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~  289 (676)
                      ....++|||+|||+++++++|+++|++||.|. +.++.+..+   |+++|||||+|.+.++|++|++.|+  .+.|+.|.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEE
Confidence            34568999999999999999999999999999 888888776   7899999999999999999999883  25555555


Q ss_pred             EEEe
Q 005812          290 VDWA  293 (676)
Q Consensus       290 v~~a  293 (676)
                      +..+
T Consensus        82 ~~~~   85 (114)
T 2dnl_A           82 CVSS   85 (114)
T ss_dssp             EECC
T ss_pred             eccC
Confidence            5543

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.44  E-value=2.4e-13  Score=111.82  Aligned_cols=71  Identities=28%  Similarity=0.543  Sum_probs=65.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhC----C-------ceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCC
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAF----G-------EVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSG  492 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~----G-------~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~  492 (676)
                      +.++|||+|||+.+++++|+++|++|    |       .|.++.+..+      +|||||+|.+.++|.+|+ .||    
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~----   73 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFD----   73 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGT----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcC----
Confidence            45899999999999999999999999    8       8999987643      799999999999999999 999    


Q ss_pred             CCeeecCcEEEEEE
Q 005812          493 LGIFLKGRQLTVLK  506 (676)
Q Consensus       493 ~g~~l~gr~l~v~~  506 (676)
                       +..|+|+.|.|.+
T Consensus        74 -g~~~~g~~l~V~r   86 (87)
T 2hzc_A           74 -GIIFQGQSLKIRR   86 (87)
T ss_dssp             -TCEETTEECEEEC
T ss_pred             -CCEECCeEEEEeC
Confidence             9999999999974

>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

Probab=99.43  E-value=1.2e-13  Score=119.94  Aligned_cols=75  Identities=20%  Similarity=0.241  Sum_probs=66.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE--
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ--  501 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~--  501 (676)
                      ..++|||.|||+.+++++|+++|++||.|..|.|+.+       |||||+|.+.++|.+|++.||     +..|+|+.  
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~-----g~~~~gr~~~   82 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLD-----NTKFRSHEGE   82 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHT-----TCBCCCTTSC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhC-----CCEECCcEee
Confidence            3589999999999999999999999999999988654       899999999999999999999     99999998  


Q ss_pred             ---EEEEEccCc
Q 005812          502 ---LTVLKALDK  510 (676)
Q Consensus       502 ---l~v~~a~~k  510 (676)
                         |.|..+.++
T Consensus        83 ~~~i~v~~~~~~   94 (115)
T 3beg_B           83 TAYIRVKVDGPR   94 (115)
T ss_dssp             CCBCEEEECC--
T ss_pred             eEEEEeccCCCC
Confidence               777776553

>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

Probab=99.42  E-value=2.2e-13  Score=118.41  Aligned_cols=76  Identities=22%  Similarity=0.380  Sum_probs=67.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCee-----E
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRP-----I  288 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~-----i  288 (676)
                      ...++|||+|||+++++++|+++|+.||.|..|.|+.+       |||||+|.+.++|++||+.|||..|.|+.     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            45689999999999999999999999999999999875       89999999999999999999999999998     7


Q ss_pred             EEEEecCC
Q 005812          289 AVDWAVPK  296 (676)
Q Consensus       289 ~v~~a~~~  296 (676)
                      .|..+.+.
T Consensus        87 ~v~~~~~~   94 (115)
T 3beg_B           87 RVKVDGPR   94 (115)
T ss_dssp             EEEECC--
T ss_pred             EeccCCCC
Confidence            77776654

>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

Probab=99.40  E-value=1.9e-13  Score=112.64  Aligned_cols=75  Identities=19%  Similarity=0.349  Sum_probs=65.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|++||.|..|+++.+     ++|||||+|.+.++|.+|+..       .+.+.|+.|.|
T Consensus         5 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-------~~~~~g~~l~v   72 (88)
T 1wf0_A            5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-------DLIIKGISVHI   72 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-------EEEETTEEEEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-------CceeCCEEEEE
Confidence            589999999999999999999999999999988754     689999999999999754221       46779999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .++.++.
T Consensus        73 ~~a~~~~   79 (88)
T 1wf0_A           73 SNAEPKH   79 (88)
T ss_dssp             ECCCCCC
T ss_pred             EecCCCC
Confidence            9998764

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.40  E-value=5e-13  Score=109.87  Aligned_cols=72  Identities=28%  Similarity=0.511  Sum_probs=66.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccC----C-------ceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCce
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPV----G-------LVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK  282 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~----G-------~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~  282 (676)
                      ...++|||+|||+++++++|+++|+.|    |       .|.++.+..      .+|||||+|.+.++|.+|+ .|||..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~------~kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECS------SSSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecC------CCcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            456899999999999999999999999    8       899999986      3799999999999999999 899999


Q ss_pred             eCCeeEEEEE
Q 005812          283 FGKRPIAVDW  292 (676)
Q Consensus       283 ~~g~~i~v~~  292 (676)
                      +.|+.|+|..
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999974

>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

Probab=99.39  E-value=4.6e-13  Score=110.32  Aligned_cols=78  Identities=23%  Similarity=0.326  Sum_probs=66.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ...++|||+|||+++++++|+++|++||.|.+|.|+.+     ++|||||+|.+.++|++|+..  ...+.|+.|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEec
Confidence            35689999999999999999999999999999999875     789999999999999864331  34458999999999


Q ss_pred             cCCCC
Q 005812          294 VPKNI  298 (676)
Q Consensus       294 ~~~~~  298 (676)
                      .++..
T Consensus        76 ~~~~~   80 (88)
T 1wf0_A           76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.39  E-value=1.1e-12  Score=124.79  Aligned_cols=78  Identities=23%  Similarity=0.314  Sum_probs=71.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+++++++|+++|++||.|..|+++++. ++.++|||||+|.+.++|.+|+..++      ..|+|++|.|
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~------~~~~Gr~l~V  181 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG------QKYKETDLLI  181 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT------CEETTEECEE
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCC------CeECCEEEEE
Confidence            4899999999999999999999999999999998875 58899999999999999999997765      5999999999


Q ss_pred             EEccC
Q 005812          505 LKALD  509 (676)
Q Consensus       505 ~~a~~  509 (676)
                      .++..
T Consensus       182 ~~~~~  186 (193)
T 2voo_A          182 LFKDD  186 (193)
T ss_dssp             EETTT
T ss_pred             EEhHH
Confidence            98654

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.38  E-value=9.6e-13  Score=111.84  Aligned_cols=83  Identities=19%  Similarity=0.174  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCC--CCCCC--------HHHHHHHHHhCCceeEEEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHcCCC
Q 005812          423 ELQNTIFICNL--PFDLD--------NEEVKQRFSAFGEVVSFVPVLHQVT--KRPKGTGFLKFKTVEAATAAVSASKTT  490 (676)
Q Consensus       423 ~~~~~l~V~nL--p~~~t--------eedl~~~F~~~G~v~~v~i~~~~~~--~~~~g~afV~F~t~~~A~~Al~~l~~~  490 (676)
                      .++++|.|+||  |.++.        ++||++.|++||.|.+|.|+++..+  +.++|+|||+|.++++|.+|+..||  
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~ln--   80 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLT--   80 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHT--
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhC--
Confidence            35689999999  44443        4799999999999999999887654  3679999999999999999999999  


Q ss_pred             CCCCeeecCcEEEEEEccCc
Q 005812          491 SGLGIFLKGRQLTVLKALDK  510 (676)
Q Consensus       491 ~~~g~~l~gr~l~v~~a~~k  510 (676)
                         |..|+||.|.|.++...
T Consensus        81 ---G~~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           81 ---GRKFANRVVVTKYCDPD   97 (105)
T ss_dssp             ---TCEETTEECEEEEECHH
T ss_pred             ---CCEeCCCEEEEEEeCHH
Confidence               99999999999997643

>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

Probab=99.35  E-value=4.1e-12  Score=109.73  Aligned_cols=81  Identities=21%  Similarity=0.386  Sum_probs=69.5

Q ss_pred             CCCCCeEEEcCCCCCCC-----------HHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCC
Q 005812          422 DELQNTIFICNLPFDLD-----------NEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTT  490 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~t-----------eedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~  490 (676)
                      ..++++|+|+||.....           +++|+++|++||.|..|.| .+.   .++|||||+|.+.++|.+|+..||  
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~ln--   85 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLD--   85 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHST--
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcC--
Confidence            34578999999944332           6899999999999999955 553   379999999999999999999999  


Q ss_pred             CCCCeeecCcEEEEEEccCch
Q 005812          491 SGLGIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       491 ~~~g~~l~gr~l~v~~a~~k~  511 (676)
                         |..|+||+|.|.++.++.
T Consensus        86 ---g~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           86 ---GRWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             ---TCEETTEECEEEECCSCC
T ss_pred             ---CCEECCcEEEEEEeCCCC
Confidence               999999999999988754

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.35  E-value=1.9e-12  Score=112.09  Aligned_cols=81  Identities=17%  Similarity=0.219  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCC--CCC---CHHHHHHHHHhCCceeEEEEeecCC----CCCcceEEEEEeCCHHHHHHHHHHcCCCCCCC
Q 005812          424 LQNTIFICNLP--FDL---DNEEVKQRFSAFGEVVSFVPVLHQV----TKRPKGTGFLKFKTVEAATAAVSASKTTSGLG  494 (676)
Q Consensus       424 ~~~~l~V~nLp--~~~---teedl~~~F~~~G~v~~v~i~~~~~----~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g  494 (676)
                      ++++|+|+||-  .++   .++||++.|++||.|.+|.|+.+..    ++.++|+|||+|.++++|.+|+..||     |
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~Ln-----G   93 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN-----G   93 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHT-----T
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHC-----C
Confidence            56899999993  223   3789999999999999999998854    35678999999999999999999999     9


Q ss_pred             eeecCcEEEEEEccC
Q 005812          495 IFLKGRQLTVLKALD  509 (676)
Q Consensus       495 ~~l~gr~l~v~~a~~  509 (676)
                      ..|+||.|.|.++..
T Consensus        94 r~f~GR~i~v~~~~~  108 (118)
T 3ue2_A           94 RWFAGRKVVAEVYDQ  108 (118)
T ss_dssp             CEETTEECEEEEECH
T ss_pred             CEECCcEEEEEEcCh
Confidence            999999999999754

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.33  E-value=1.4e-12  Score=126.84  Aligned_cols=78  Identities=26%  Similarity=0.294  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCCCC---------CHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCC
Q 005812          423 ELQNTIFICNLPFDL---------DNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGL  493 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~---------teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~  493 (676)
                      ...++|||+|||..+         ++++|+++|++||.|.+|+|+.      ++|||||+|.+.++|..|+.+|+     
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~-----  200 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMS-----  200 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHT-----
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhC-----
Confidence            346899999999998         7999999999999999999874      38999999999999999999999     


Q ss_pred             Ceee------------cCcEEEEEEccCch
Q 005812          494 GIFL------------KGRQLTVLKALDKK  511 (676)
Q Consensus       494 g~~l------------~gr~l~v~~a~~k~  511 (676)
                      |..|            .|+.|.|.||....
T Consensus       201 g~~l~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          201 NQTLLLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             TCCCCCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             CCEEeccccccccccCCCCEEEEEEccCCC
Confidence            9999            89999999998754

>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

Probab=99.33  E-value=6.8e-12  Score=108.34  Aligned_cols=84  Identities=21%  Similarity=0.311  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEcCCCCCCC-----------HHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCC
Q 005812          212 SKTQKWKLIIRNIPFKAK-----------VNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNG  280 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~-----------e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~  280 (676)
                      .+...++|+|+||.....           +++|+++|++||.|.+|.| .++   .++|||||+|.+.++|.+|+..|||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            456788999999954432           6899999999999999976 432   2789999999999999999999999


Q ss_pred             ceeCCeeEEEEEecCCCCC
Q 005812          281 QKFGKRPIAVDWAVPKNIY  299 (676)
Q Consensus       281 ~~~~g~~i~v~~a~~~~~~  299 (676)
                      ..|.|+.|.|.|+.++..+
T Consensus        87 ~~~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             CEETTEECEEEECCSCCCS
T ss_pred             CEECCcEEEEEEeCCCCCc
Confidence            9999999999999876544

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.32  E-value=1.9e-12  Score=125.83  Aligned_cols=79  Identities=24%  Similarity=0.304  Sum_probs=71.4

Q ss_pred             CCCCcEEEEcCCCCCC---------CHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 005812          213 KTQKWKLIIRNIPFKA---------KVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF  283 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~---------~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  283 (676)
                      ....++|||+|||..+         ++++|+.+|++||.|.+|+|+.      ++|||||+|.+.++|+.|++.|+|..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4467899999999998         7999999999999999999986      579999999999999999999999999


Q ss_pred             ------------CCeeEEEEEecCCC
Q 005812          284 ------------GKRPIAVDWAVPKN  297 (676)
Q Consensus       284 ------------~g~~i~v~~a~~~~  297 (676)
                                  .|+.|.|.|+.+..
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             eccccccccccCCCCEEEEEEccCCC
Confidence                        89999999997654

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.30  E-value=5.3e-12  Score=107.20  Aligned_cols=82  Identities=30%  Similarity=0.447  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCC--CCCCC--------HHHHHHhhccCCceEEEEEcccCCC--CCceeEEEEEecCHHHHHHHHHHhCCc
Q 005812          214 TQKWKLIIRNI--PFKAK--------VNEIKDMFSPVGLVWNVYIPHNTDT--GLSKGFAFVKFTCKRDAESAIQKFNGQ  281 (676)
Q Consensus       214 ~~~~~v~V~nL--p~~~~--------e~~l~~~F~~~G~i~~v~i~~~~~~--~~~~g~afV~f~~~~~A~~A~~~l~~~  281 (676)
                      .+++.|.+.|+  |..+.        +++|++.|++||.|.+|.|+++..+  +.++|||||+|.+.++|.+|++.|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            35678999998  43443        4799999999999999999988654  367899999999999999999999999


Q ss_pred             eeCCeeEEEEEecC
Q 005812          282 KFGKRPIAVDWAVP  295 (676)
Q Consensus       282 ~~~g~~i~v~~a~~  295 (676)
                      .|.|+.|.|.++.+
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999999854

>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

Probab=99.26  E-value=2.4e-12  Score=109.27  Aligned_cols=72  Identities=22%  Similarity=0.318  Sum_probs=64.4

Q ss_pred             EcCCCCCCCHHHHHHhh------------ccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeE
Q 005812          221 IRNIPFKAKVNEIKDMF------------SPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPI  288 (676)
Q Consensus       221 V~nLp~~~~e~~l~~~F------------~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i  288 (676)
                      +.|||+.+++++|+++|            ++||.|.+|.|+++. +++++|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56777778888777666            999999999999876 47899999999999999999999999999999999


Q ss_pred             EEEEe
Q 005812          289 AVDWA  293 (676)
Q Consensus       289 ~v~~a  293 (676)
                      .|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99987

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.26  E-value=1.6e-11  Score=106.27  Aligned_cols=81  Identities=21%  Similarity=0.254  Sum_probs=71.1

Q ss_pred             CCcEEEEcCCCC--CC---CHHHHHHhhccCCceEEEEEcccCC----CCCceeEEEEEecCHHHHHHHHHHhCCceeCC
Q 005812          215 QKWKLIIRNIPF--KA---KVNEIKDMFSPVGLVWNVYIPHNTD----TGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK  285 (676)
Q Consensus       215 ~~~~v~V~nLp~--~~---~e~~l~~~F~~~G~i~~v~i~~~~~----~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g  285 (676)
                      ++++|+++|+-.  .+   -+++|++.|++||.|.+|.|++++.    ++.++|||||+|.+.++|.+|++.|||..|.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            567999999942  22   3789999999999999999998764    35678999999999999999999999999999


Q ss_pred             eeEEEEEecC
Q 005812          286 RPIAVDWAVP  295 (676)
Q Consensus       286 ~~i~v~~a~~  295 (676)
                      +.|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999854

>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

Probab=99.26  E-value=2.6e-12  Score=109.04  Aligned_cols=72  Identities=18%  Similarity=0.276  Sum_probs=63.2

Q ss_pred             EcCCCCCCCHHHHHHHH------------HhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee
Q 005812          430 ICNLPFDLDNEEVKQRF------------SAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL  497 (676)
Q Consensus       430 V~nLp~~~teedl~~~F------------~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l  497 (676)
                      +.|||..+++++|+++|            ++||.|.+|.|+++. .+.++|||||+|.++++|.+|+..||     |..+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~ln-----g~~~   93 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLN-----NRWF   93 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHT-----TCEE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHC-----CCEE
Confidence            45677777777777666            999999999998875 47899999999999999999999999     9999


Q ss_pred             cCcEEEEEEc
Q 005812          498 KGRQLTVLKA  507 (676)
Q Consensus       498 ~gr~l~v~~a  507 (676)
                      +||+|.|.++
T Consensus        94 ~Gr~i~v~~s  103 (104)
T 1jmt_A           94 NGQPIHAELS  103 (104)
T ss_dssp             TTEECCEEEC
T ss_pred             CCEEEEEEEc
Confidence            9999999986

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

Probab=99.16  E-value=1.1e-10  Score=97.66  Aligned_cols=75  Identities=21%  Similarity=0.244  Sum_probs=64.0

Q ss_pred             CCeEEEcCCC-------CCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee
Q 005812          425 QNTIFICNLP-------FDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL  497 (676)
Q Consensus       425 ~~~l~V~nLp-------~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l  497 (676)
                      .++|.|.-..       ..+++++|+++|++||.|..|.|+     +.++|||||+|.+.++|..|+..++     +  +
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~-----~--~   77 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV-----G--L   77 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC-----B--C
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC-----C--C
Confidence            3567776654       458999999999999999999887     3679999999999999999999876     4  5


Q ss_pred             cCcEEEEEEccCch
Q 005812          498 KGRQLTVLKALDKK  511 (676)
Q Consensus       498 ~gr~l~v~~a~~k~  511 (676)
                      .|++|.|.|+.++.
T Consensus        78 ~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           78 VDNPLKISWLEGQP   91 (100)
T ss_dssp             SSSBCEEECSSCCC
T ss_pred             CCCeEEEEEccCCC
Confidence            79999999988764

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.15  E-value=9.9e-11  Score=100.53  Aligned_cols=79  Identities=19%  Similarity=0.223  Sum_probs=67.1

Q ss_pred             CCCCeEEEcCCCC--CC--------CHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCC
Q 005812          423 ELQNTIFICNLPF--DL--------DNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSG  492 (676)
Q Consensus       423 ~~~~~l~V~nLp~--~~--------teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~  492 (676)
                      .++++|.|+||=.  +.        .++||++.|++||.|.+|.|.++.    ++|+|||+|.+.++|.+|+..||    
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~ln----   76 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALH----   76 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHT----
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhC----
Confidence            4568999999922  21        256899999999999999886542    58999999999999999999999    


Q ss_pred             CCeeecCcEEEEEEccCc
Q 005812          493 LGIFLKGRQLTVLKALDK  510 (676)
Q Consensus       493 ~g~~l~gr~l~v~~a~~k  510 (676)
                       |..|+||.|.|.++...
T Consensus        77 -G~~f~GR~i~v~~~~~~   93 (114)
T 3s6e_A           77 -GRWFAGKMITAAYVPLP   93 (114)
T ss_dssp             -TCEETTEECEEEEECHH
T ss_pred             -CCEECCEEEEEEEEcHH
Confidence             99999999999998643

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.13  E-value=2.1e-10  Score=98.44  Aligned_cols=79  Identities=16%  Similarity=0.247  Sum_probs=67.9

Q ss_pred             CCCCcEEEEcCCCCCC----------CHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCce
Q 005812          213 KTQKWKLIIRNIPFKA----------KVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK  282 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~----------~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~  282 (676)
                      +.+.++|.++|+=...          -+++|++.|++||.|.+|.|+++.    .+|||||+|.+.++|.+|++.|||..
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~   79 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRW   79 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCE
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4567789999983322          146889999999999999998763    58999999999999999999999999


Q ss_pred             eCCeeEEEEEecC
Q 005812          283 FGKRPIAVDWAVP  295 (676)
Q Consensus       283 ~~g~~i~v~~a~~  295 (676)
                      |.|+.|.|.|+..
T Consensus        80 f~GR~i~v~~~~~   92 (114)
T 3s6e_A           80 FAGKMITAAYVPL   92 (114)
T ss_dssp             ETTEECEEEEECH
T ss_pred             ECCEEEEEEEEcH
Confidence            9999999999854

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

Probab=99.13  E-value=2.8e-10  Score=95.24  Aligned_cols=75  Identities=21%  Similarity=0.260  Sum_probs=62.6

Q ss_pred             CcEEEEcCCC-------CCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeE
Q 005812          216 KWKLIIRNIP-------FKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPI  288 (676)
Q Consensus       216 ~~~v~V~nLp-------~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i  288 (676)
                      ..+|.|.-.+       ..+++++|+++|++||.|.+|.|+.     .++|||||+|.+.++|..|++.+++  +.|+.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~-----~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS-----KKPGTAVVEFATVKAAELAVQNEVG--LVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEES-----SSSSEEEEEESCHHHHHHHHHTCCB--CSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEcc-----CCCCEEEEEECCHHHHHHHHHhcCC--CCCCeE
Confidence            3455555443       4689999999999999999999983     4889999999999999999997544  679999


Q ss_pred             EEEEecCCC
Q 005812          289 AVDWAVPKN  297 (676)
Q Consensus       289 ~v~~a~~~~  297 (676)
                      .|.|+.++.
T Consensus        83 ~V~~a~~~~   91 (100)
T 2d9o_A           83 KISWLEGQP   91 (100)
T ss_dssp             EEECSSCCC
T ss_pred             EEEEccCCC
Confidence            999997654

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.07  E-value=2.4e-10  Score=117.16  Aligned_cols=77  Identities=16%  Similarity=0.169  Sum_probs=66.1

Q ss_pred             CCCCCCeEEEcC--CCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec
Q 005812          421 EDELQNTIFICN--LPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK  498 (676)
Q Consensus       421 ~~~~~~~l~V~n--Lp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~  498 (676)
                      ...++.+|||+|  |++.+|+++|+++|++||.|.+|.+..      ++|||||+|.+.++|.+|++.||     |..+.
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~ln-----G~~~~   82 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLN-----GKEVV   82 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTT-----TCEEE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhC-----CCccc
Confidence            355678999999  588999999999999999999986532      47999999999999999999999     88773


Q ss_pred             ---Cc--EEEEEEcc
Q 005812          499 ---GR--QLTVLKAL  508 (676)
Q Consensus       499 ---gr--~l~v~~a~  508 (676)
                         |+  +|.|.++.
T Consensus        83 ~~~g~~~~ly~~~~~   97 (345)
T 3tht_A           83 DDLGQKITLYLNFVE   97 (345)
T ss_dssp             CTTSCEEECEEEECS
T ss_pred             cccCCceEEEEEEee
Confidence               45  68888874

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.05  E-value=3.4e-10  Score=116.13  Aligned_cols=77  Identities=16%  Similarity=0.336  Sum_probs=67.2

Q ss_pred             CCCCCcEEEEcC--CCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee---CCe
Q 005812          212 SKTQKWKLIIRN--IPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF---GKR  286 (676)
Q Consensus       212 ~~~~~~~v~V~n--Lp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~---~g~  286 (676)
                      ...+..+|||+|  |+..+++++|+++|++||.|.+|.++.      ++|||||+|.+.++|++|++.|||..+   .|+
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~   87 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   87 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCC
Confidence            355678999999  578999999999999999999998865      579999999999999999999999987   345


Q ss_pred             --eEEEEEec
Q 005812          287 --PIAVDWAV  294 (676)
Q Consensus       287 --~i~v~~a~  294 (676)
                        .|.|.++.
T Consensus        88 ~~~ly~~~~~   97 (345)
T 3tht_A           88 KITLYLNFVE   97 (345)
T ss_dssp             EEECEEEECS
T ss_pred             ceEEEEEEee
Confidence              67888874

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.93  E-value=1.6e-09  Score=92.97  Aligned_cols=78  Identities=17%  Similarity=0.135  Sum_probs=68.2

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCC-HHHHHHHHHHcCCCCCCCeeecC
Q 005812          422 DELQNTIFICNLPFD-LDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKT-VEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~-~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t-~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      -.+++.|+|.||+.. +++++|+++|+.||.|.+|.+..+..      .|||+|.+ +.+|..|+..|+.   ++..|.|
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~---~~~~i~g   85 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANN---GNLQLRN   85 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTT---SCBCTTS
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhc---CCcEEeC
Confidence            345899999999999 99999999999999999998876632      59999999 7999999999963   3899999


Q ss_pred             cEEEEEEcc
Q 005812          500 RQLTVLKAL  508 (676)
Q Consensus       500 r~l~v~~a~  508 (676)
                      ..+++....
T Consensus        86 ~~~~~evL~   94 (121)
T 1owx_A           86 KEVTWEVLE   94 (121)
T ss_dssp             SSEEEEECC
T ss_pred             cEEEEEECC
Confidence            999887754

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.87  E-value=6.5e-09  Score=83.21  Aligned_cols=73  Identities=22%  Similarity=0.272  Sum_probs=62.1

Q ss_pred             CCCCeEEEcCCC----CCCCH----HHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCC
Q 005812          423 ELQNTIFICNLP----FDLDN----EEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLG  494 (676)
Q Consensus       423 ~~~~~l~V~nLp----~~~te----edl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g  494 (676)
                      ++..||+|...|    ..+..    .+|.+.|++||.|..++++.+.        +||+|.+.++|.+|+. ||     |
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mn-----G   70 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LN-----G   70 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GT-----T
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cC-----C
Confidence            345788888776    23433    6789999999999999998763        8999999999999998 99     9


Q ss_pred             eeecCcEEEEEEccC
Q 005812          495 IFLKGRQLTVLKALD  509 (676)
Q Consensus       495 ~~l~gr~l~v~~a~~  509 (676)
                      ..++||.|+|.++.+
T Consensus        71 ~~v~Gr~LkV~lkt~   85 (91)
T 2dnr_A           71 KELLNRTITIALKSP   85 (91)
T ss_dssp             CEETTEEEEEEECCC
T ss_pred             eEeCCeEEEEEeCCC
Confidence            999999999999765

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.82  E-value=1.6e-08  Score=80.98  Aligned_cols=76  Identities=16%  Similarity=0.230  Sum_probs=64.8

Q ss_pred             CCCCcEEEEcCCC----CCCCH----HHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC
Q 005812          213 KTQKWKLIIRNIP----FKAKV----NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFG  284 (676)
Q Consensus       213 ~~~~~~v~V~nLp----~~~~e----~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~  284 (676)
                      .++..+|+|.-.|    ..+-.    .+|.+.|++||.|..++++.+.        +||+|.+.++|.+|++ |||..++
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~   74 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELL   74 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEET
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeC
Confidence            3456788888876    23333    6789999999999999999864        8999999999999999 9999999


Q ss_pred             CeeEEEEEecCCC
Q 005812          285 KRPIAVDWAVPKN  297 (676)
Q Consensus       285 g~~i~v~~a~~~~  297 (676)
                      |+.|+|.++.|.-
T Consensus        75 Gr~LkV~lkt~dW   87 (91)
T 2dnr_A           75 NRTITIALKSPSG   87 (91)
T ss_dssp             TEEEEEEECCCSS
T ss_pred             CeEEEEEeCCCCc
Confidence            9999999987653

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.80  E-value=2.2e-08  Score=85.90  Aligned_cols=77  Identities=9%  Similarity=0.036  Sum_probs=68.6

Q ss_pred             CCCCCCcEEEEcCCCCC-CCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecC-HHHHHHHHHHhC--CceeCCe
Q 005812          211 GSKTQKWKLIIRNIPFK-AKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC-KRDAESAIQKFN--GQKFGKR  286 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~-~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~-~~~A~~A~~~l~--~~~~~g~  286 (676)
                      ..-..++.|+|+||+.. ++.++|+++|+.||.|..|.+..+..      .|||+|.+ +.+|..|+..|+  +..|+|.
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~   86 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNK   86 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCc
Confidence            35567899999999999 99999999999999999999998653      49999999 899999999995  7788999


Q ss_pred             eEEEEEe
Q 005812          287 PIAVDWA  293 (676)
Q Consensus       287 ~i~v~~a  293 (676)
                      .+.++..
T Consensus        87 ~~~~evL   93 (121)
T 1owx_A           87 EVTWEVL   93 (121)
T ss_dssp             SEEEEEC
T ss_pred             EEEEEEC
Confidence            8888765

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.65  E-value=3.3e-08  Score=79.49  Aligned_cols=73  Identities=18%  Similarity=0.218  Sum_probs=61.6

Q ss_pred             CCCCCeEEEcCCCCC-----CCH----HHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCC
Q 005812          422 DELQNTIFICNLPFD-----LDN----EEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSG  492 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~-----~te----edl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~  492 (676)
                      .++..||+|..++..     +..    .+|.+.|+.||.|..++++.+.        +||+|.+.++|.+|+. |+    
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ld----   78 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VD----   78 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GG----
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cC----
Confidence            345679999988743     322    5689999999999999998763        9999999999999998 99    


Q ss_pred             CCeeecCcEEEEEEcc
Q 005812          493 LGIFLKGRQLTVLKAL  508 (676)
Q Consensus       493 ~g~~l~gr~l~v~~a~  508 (676)
                       |..++||.|+|.+..
T Consensus        79 -G~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           79 -GMKVKGRAVKISGPS   93 (95)
T ss_dssp             -GSEETTEEEEEECCC
T ss_pred             -CeeeCCeEEEEeccC
Confidence             999999999998743

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.59  E-value=1.2e-07  Score=92.33  Aligned_cols=78  Identities=18%  Similarity=0.201  Sum_probs=66.3

Q ss_pred             CeEEEcCCC-----CCCCHHHHHHHHHhCCceeEEEEeecCC----CCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCee
Q 005812          426 NTIFICNLP-----FDLDNEEVKQRFSAFGEVVSFVPVLHQV----TKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIF  496 (676)
Q Consensus       426 ~~l~V~nLp-----~~~teedl~~~F~~~G~v~~v~i~~~~~----~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~  496 (676)
                      ..+.+.|+-     ..-.+++|++.|++||.|.++.|+.+..    ++.++|++||+|.+.++|.+|+..||     |..
T Consensus       125 ~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~-----gr~  199 (222)
T 3dxb_A          125 TVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN-----GRW  199 (222)
T ss_dssp             SEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHT-----TCB
T ss_pred             ccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhc-----Cce
Confidence            456666662     2335789999999999999999986643    44889999999999999999999999     999


Q ss_pred             ecCcEEEEEEcc
Q 005812          497 LKGRQLTVLKAL  508 (676)
Q Consensus       497 l~gr~l~v~~a~  508 (676)
                      ++||.|.+.++.
T Consensus       200 ~~gr~i~~~~~~  211 (222)
T 3dxb_A          200 FAGRKVVAEVYD  211 (222)
T ss_dssp             SSSSBCEEEECC
T ss_pred             ECCeEEEEEEcC
Confidence            999999999965

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.54  E-value=1.8e-07  Score=91.11  Aligned_cols=67  Identities=22%  Similarity=0.266  Sum_probs=60.7

Q ss_pred             CCHHHHHHhhccCCceEEEEEcccC----CCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          228 AKVNEIKDMFSPVGLVWNVYIPHNT----DTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       228 ~~e~~l~~~F~~~G~i~~v~i~~~~----~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      -.+++|++.|++||.|.++.|+++.    .++.++|++||+|.+.++|.+|++.|||..+.||.|.+.++.
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            4578999999999999999998554    345899999999999999999999999999999999999984

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.49  E-value=8e-08  Score=77.22  Aligned_cols=74  Identities=15%  Similarity=0.184  Sum_probs=63.1

Q ss_pred             CCCCCcEEEEcCCCCC-----C-CH---HHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCce
Q 005812          212 SKTQKWKLIIRNIPFK-----A-KV---NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQK  282 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~-----~-~e---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~  282 (676)
                      ..++..+|+|.-++..     + ++   .+|.+.|..||.|..+++..++        +||+|.+.++|.+|++ |+|..
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~   81 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCee
Confidence            3456779999988743     2 31   5689999999999999999874        9999999999999999 99999


Q ss_pred             eCCeeEEEEEec
Q 005812          283 FGKRPIAVDWAV  294 (676)
Q Consensus       283 ~~g~~i~v~~a~  294 (676)
                      ++|+.|+|.+-.
T Consensus        82 v~Gr~L~V~~k~   93 (95)
T 1ufw_A           82 VKGRAVKISGPS   93 (95)
T ss_dssp             ETTEEEEEECCC
T ss_pred             eCCeEEEEeccC
Confidence            999999998754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.37  E-value=2.1e-06  Score=70.15  Aligned_cols=72  Identities=11%  Similarity=0.111  Sum_probs=66.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhC-----CceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAF-----GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~-----G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      .++|-|.|||..+++..|+.+..++     |.++.+.+..|      .+-|+|+|.+...|-+|...|+     |..|.|
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD------H~GAivef~d~~~AgKasLaL~-----G~ef~g   89 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD------FNGAIIIFRDSKFAAKMLMILN-----GSQFQG   89 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT------TTEEEEECSCHHHHHHHHHHHS-----SEEETT
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC------CCceEEEEccchhhHHHHhhcC-----CeeecC
Confidence            5799999999999999999999999     99999988766      4569999999999999999999     999999


Q ss_pred             cEEEEEEc
Q 005812          500 RQLTVLKA  507 (676)
Q Consensus       500 r~l~v~~a  507 (676)
                      |+|++.-.
T Consensus        90 r~Lr~gTv   97 (117)
T 2l9w_A           90 KVIRSGTI   97 (117)
T ss_dssp             EEEEEECH
T ss_pred             eEEEecCH
Confidence            99999753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.07  E-value=1.5e-05  Score=65.20  Aligned_cols=74  Identities=14%  Similarity=0.103  Sum_probs=67.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccC-----CceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCee
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPV-----GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRP  287 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~-----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  287 (676)
                      ....++|-+-|||..++...|+.+..+|     |.|..+.+..+.      +-|+|+|.+...|.+|.-.|+|..|.|++
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~   91 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKV   91 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeE
Confidence            3457899999999999999999999999     999999999874      33999999999999999999999999999


Q ss_pred             EEEEE
Q 005812          288 IAVDW  292 (676)
Q Consensus       288 i~v~~  292 (676)
                      |++.-
T Consensus        92 Lr~gT   96 (117)
T 2l9w_A           92 IRSGT   96 (117)
T ss_dssp             EEEEC
T ss_pred             EEecC
Confidence            99963

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.70  E-value=0.00015  Score=58.96  Aligned_cols=72  Identities=22%  Similarity=0.272  Sum_probs=60.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhC-----CceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAF-----GEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~-----G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      +.+|.|.|||..++++.|.-+|+.-     |.|..+....        +-|+|+|.+...|++.|+.-      ...|.|
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~------~H~L~~   73 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQA------DHELHG   73 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCS------CCBSSS
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCC------cceecC
Confidence            5799999999999999999999972     5788876532        56899999999999999763      368899


Q ss_pred             cEEEEEEccCc
Q 005812          500 RQLTVLKALDK  510 (676)
Q Consensus       500 r~l~v~~a~~k  510 (676)
                      ..|.|....++
T Consensus        74 ~~LsV~P~~~~   84 (104)
T 2dhx_A           74 AQLSLRPAPPR   84 (104)
T ss_dssp             SBCEEEECCCC
T ss_pred             eEEEEEcCCCC
Confidence            99999886554

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.68  E-value=0.0003  Score=57.18  Aligned_cols=74  Identities=15%  Similarity=0.137  Sum_probs=60.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhcc-C----CceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeE
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSP-V----GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPI  288 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~-~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i  288 (676)
                      ....+|.|.|||..++++.|.-+|+. -    |.|.++....        +-|+|+|.+.+.|++.|++ ....|.+..|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEE
Confidence            45679999999999999999999976 2    5688877654        2389999999999999984 4778889999


Q ss_pred             EEEEecCC
Q 005812          289 AVDWAVPK  296 (676)
Q Consensus       289 ~v~~a~~~  296 (676)
                      .|....+.
T Consensus        77 sV~P~~~~   84 (104)
T 2dhx_A           77 SLRPAPPR   84 (104)
T ss_dssp             EEEECCCC
T ss_pred             EEEcCCCC
Confidence            99876443

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.42  E-value=0.0003  Score=57.51  Aligned_cols=73  Identities=12%  Similarity=0.134  Sum_probs=62.5

Q ss_pred             CeEEEcCCCCCC-C----HHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          426 NTIFICNLPFDL-D----NEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       426 ~~l~V~nLp~~~-t----eedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ++|+|.||+..+ .    .+.++++|..|+++.....++.      -.-..|.|.++++|.+|...|+     +..+.|+
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS------FRRirv~F~~~~~A~~AR~~Lh-----~~~f~g~   74 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLH-----KTEFLGK   74 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTST-----TSEETTE
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc------ceEEEEEeCChHHHHHHHHHhc-----cceecCc
Confidence            699999999876 2    3678999999999888766643      2246899999999999999999     9999999


Q ss_pred             EEEEEEccC
Q 005812          501 QLTVLKALD  509 (676)
Q Consensus       501 ~l~v~~a~~  509 (676)
                      .|+|-++++
T Consensus        75 ~~r~YFgq~   83 (104)
T 1wey_A           75 EMKLYFAQT   83 (104)
T ss_dssp             ECEEECCCC
T ss_pred             eeEEEecCC
Confidence            999999874

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.41  E-value=0.00042  Score=56.71  Aligned_cols=76  Identities=11%  Similarity=0.020  Sum_probs=63.7

Q ss_pred             CcEEEEcCCCCCC-C----HHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          216 KWKLIIRNIPFKA-K----VNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       216 ~~~v~V~nLp~~~-~----e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      .++|+|.||+..+ .    .+.++.+|..|+.+......+.      =.-..|.|.++++|.+|...|++..+.|+.|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS------FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc------ceEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            4689999998854 2    2678999999999888777663      223789999999999999999999999999999


Q ss_pred             EEecCCC
Q 005812          291 DWAVPKN  297 (676)
Q Consensus       291 ~~a~~~~  297 (676)
                      .++.+..
T Consensus        79 YFgq~~~   85 (104)
T 1wey_A           79 YFAQTLH   85 (104)
T ss_dssp             ECCCCSS
T ss_pred             EecCCCC
Confidence            9997543

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.32  E-value=0.00077  Score=54.28  Aligned_cols=84  Identities=13%  Similarity=0.107  Sum_probs=65.9

Q ss_pred             CeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCC
Q 005812          578 TRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNN  657 (676)
Q Consensus       578 ~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~  657 (676)
                      ++|.||+||..+|++++.+.+.         ..+.+...........    ........|+|.|.+.+++..-.+.++|+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~---------~~~~~d~~~fv~G~~s----~~~~~~SRaYi~f~~~e~v~~f~~~~~g~   68 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQ---------PMPEHDYFEFFSNDTS----LYPHMYARAYINFKNQEDIILFRDRFDGY   68 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHC---------SCCCEEEEEEEESCCS----STTCCCEEEEEEESSSHHHHHHHHHHTTC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhc---------CcccceEEEEeCCccC----CCCCcceEEEEEeCCHHHHHHHHHHhCCc
Confidence            5799999999999999999998         4666665555444322    23345589999999999999999999998


Q ss_pred             CC--CCCcccCcccccccc
Q 005812          658 PS--KLFYHHCFDAADAQC  674 (676)
Q Consensus       658 ~~--~~~~~~~~~~~~~~~  674 (676)
                      ..  .-|-..+++|.+|..
T Consensus        69 ~F~D~kg~~~~a~VE~AP~   87 (91)
T 1uw4_A           69 VFLDNKGQEYPAIVEFAPF   87 (91)
T ss_dssp             EEECTTCCEEECEEEECSS
T ss_pred             EEEcCCCCEeeeEEEEcCC
Confidence            65  446677888888864

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.08  E-value=0.0018  Score=51.97  Aligned_cols=59  Identities=17%  Similarity=0.266  Sum_probs=48.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhC
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN  279 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  279 (676)
                      .....+.++| ++|..+.-.||.++|+.||.|. |+++-|       .-|||.|.+++.|..|+..+.
T Consensus        12 ~p~r~HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~WidD-------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           12 QPKRDHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCCeEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            3445667777 9999999999999999999765 666655       249999999999999999753

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.84  E-value=0.0036  Score=50.22  Aligned_cols=60  Identities=18%  Similarity=0.300  Sum_probs=48.8

Q ss_pred             cCCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHc
Q 005812          576 SRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLN  655 (676)
Q Consensus       576 ~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~ln  655 (676)
                      ++..|++-++|..+...||.++|+         +||.|. |+++-|             ..|||-|.+++.|..||..++
T Consensus        14 ~r~HVf~l~FP~ewKt~DI~~lFs---------~fggv~-I~WidD-------------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           14 KRDHVLHVTFPKEWKTSDLYQLFS---------AFGNIQ-ISWIDD-------------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHT---------TTCSCC-CEEEET-------------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCeEEEEeCChhhhhHHHHHHhh---------ccCCEE-EEEEcC-------------CeEEEEecCHHHHHHHHHhcc
Confidence            334444449999999999999999         698665 888755             489999999999999999986


Q ss_pred             CCC
Q 005812          656 NNP  658 (676)
Q Consensus       656 g~~  658 (676)
                      -++
T Consensus        71 k~~   73 (100)
T 1whv_A           71 YAE   73 (100)
T ss_dssp             HCC
T ss_pred             cCC
Confidence            443

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.84  E-value=0.0037  Score=50.27  Aligned_cols=68  Identities=16%  Similarity=0.209  Sum_probs=57.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCC--cceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKR--PKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK  498 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~--~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~  498 (676)
                      ..|.|++||+.+|++++.+.++.++.+.....+..+.+..  ...-|||.|.+.+++......++     |..|-
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~-----g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFD-----GYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHT-----TCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhC-----CcEEE
Confidence            4799999999999999999999999888877766553322  34679999999999999999999     77664

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.61  E-value=0.0046  Score=52.07  Aligned_cols=74  Identities=18%  Similarity=0.294  Sum_probs=60.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC-eeEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK-RPIAVD  291 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g-~~i~v~  291 (676)
                      ....+.|.|-+.|... ...|..+|++||.|.+.....      ...+-.|.|.++.+|++||.+ ||..|.| ..|-|.
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV~   92 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSK-DGRIFGESIMIGVK   92 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTT-TTCEETTTEECEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEEE
Confidence            4457889999999885 578889999999999887632      346899999999999999996 9999975 667777


Q ss_pred             Eec
Q 005812          292 WAV  294 (676)
Q Consensus       292 ~a~  294 (676)
                      +..
T Consensus        93 p~~   95 (119)
T 1wwh_A           93 PCI   95 (119)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            643

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.51  E-value=0.0019  Score=51.96  Aligned_cols=55  Identities=18%  Similarity=0.275  Sum_probs=46.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN  279 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  279 (676)
                      .+.++| ++|..+.-.||.++|+.||.|. |.++-|       .-|||.|.+++.|..|+..+.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fggv~-I~WidD-------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDD-------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSEEEE-EEEEET-------TEEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccCCEE-EEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            356667 9999999999999999999554 777665       249999999999999999764

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.35  E-value=0.018  Score=48.43  Aligned_cols=70  Identities=10%  Similarity=0.018  Sum_probs=55.9

Q ss_pred             ccCcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeec
Q 005812          119 RVARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIK  198 (676)
Q Consensus       119 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~  198 (676)
                      ...+.|.|-+.|... ...|...|+.||.|.+...+               .....-+|.|.+..+|++||. .||..+.
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~---------------~~~NWihI~Y~s~~~A~rAL~-kNG~ii~   84 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS---------------NTGNWMHIRYQSKLQARKALS-KDGRIFG   84 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC---------------SSSSEEEEEESSHHHHHHHHT-TTTCEET
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC---------------CCCCeEEEEeCCHHHHHHHHH-hCCeEec
Confidence            345689999999986 56688899999999998842               224578999999999999998 5999998


Q ss_pred             Ce-EEEEe
Q 005812          199 GG-TVWAR  205 (676)
Q Consensus       199 ~~-~i~v~  205 (676)
                      |. .|-+.
T Consensus        85 g~~mIGV~   92 (119)
T 1wwh_A           85 ESIMIGVK   92 (119)
T ss_dssp             TTEECEEE
T ss_pred             CCEEEEEE
Confidence            64 34444

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.25  E-value=0.011  Score=47.83  Aligned_cols=78  Identities=17%  Similarity=0.192  Sum_probs=55.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCC--CceeEEEEEecCHHHHHHHHHHhCCceeC---C--eeE
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTG--LSKGFAFVKFTCKRDAESAIQKFNGQKFG---K--RPI  288 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~A~~~l~~~~~~---g--~~i  288 (676)
                      .-+|.|+.||+.+||+++.+.++.+-.+..........+.  ..-.-|||.|.+.++.....+.++|..|-   |  -+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            4579999999999999999988876554433332221111  12234899999999999999999999883   2  244


Q ss_pred             EEEEe
Q 005812          289 AVDWA  293 (676)
Q Consensus       289 ~v~~a  293 (676)
                      .|++|
T Consensus        89 ~VE~A   93 (97)
T 2l08_A           89 VVEFA   93 (97)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            56776

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=95.89  E-value=0.0078  Score=48.47  Aligned_cols=56  Identities=20%  Similarity=0.303  Sum_probs=47.2

Q ss_pred             eEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCC
Q 005812          579 RLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP  658 (676)
Q Consensus       579 ~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~  658 (676)
                      .++| ++|..+...||..+|+         +||.|. |+++-|             ..|||-|.+++.|..||..++-++
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs---------~fggv~-I~WidD-------------TsAlvvf~~~~~a~~al~~i~~~~   63 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFS---------AFGNIQ-ISWIDD-------------TSAFVSLSQPEQVKIAVNTSKYAE   63 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTT---------TSEEEE-EEEEET-------------TEEEEEEEEECHHHHHHHHHTTCS
T ss_pred             EEEE-eCChhhhhHHHHHHHh---------ccCCEE-EEEEcC-------------CeEEEEecCHHHHHHHHHhcccCC
Confidence            3555 9999999999999999         699654 777755             489999999999999999997544

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.72  E-value=0.008  Score=51.30  Aligned_cols=79  Identities=13%  Similarity=0.164  Sum_probs=57.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEE-EEEcccC------------CCC-CceeEEEEEecCHHHHHHHHHHhCC
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWN-VYIPHNT------------DTG-LSKGFAFVKFTCKRDAESAIQKFNG  280 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~-v~i~~~~------------~~~-~~~g~afV~f~~~~~A~~A~~~l~~  280 (676)
                      ....|.|-+.|.... ..+...|++||.|.+ +...+..            ... ....+..|+|.++.+|.+||.. ||
T Consensus         6 ~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG   83 (132)
T 3p3d_A            6 GELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NG   83 (132)
T ss_dssp             --CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TT
T ss_pred             CceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CC
Confidence            456788999977665 577789999999876 2222100            000 1346789999999999999996 99


Q ss_pred             ceeCCeeEEEEEecC
Q 005812          281 QKFGKRPIAVDWAVP  295 (676)
Q Consensus       281 ~~~~g~~i~v~~a~~  295 (676)
                      ..|.|..|-|.+..+
T Consensus        84 ~ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           84 AVFNGVLLGVIPYTK   98 (132)
T ss_dssp             CEETTEECEEEECCH
T ss_pred             eEeCcEEEEEEECCH
Confidence            999999888887744

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.16  E-value=0.021  Score=46.08  Aligned_cols=69  Identities=12%  Similarity=0.187  Sum_probs=52.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCC--cceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKR--PKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK  498 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~--~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~  498 (676)
                      +-.|.|+.||+.+|++++.+.++..-.+.+...+..+.+..  .-.-|||.|.+.++.....+..+     |..|-
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~-----g~~F~   79 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFD-----GYIFL   79 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHST-----TEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcC-----CcEEE
Confidence            35799999999999999998888765655544433322221  23568999999999999999999     77774

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=93.71  E-value=0.059  Score=45.98  Aligned_cols=76  Identities=17%  Similarity=0.241  Sum_probs=55.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEE-Eeec------------CCCC-CcceEEEEEeCCHHHHHHHHHHcCCCC
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFV-PVLH------------QVTK-RPKGTGFLKFKTVEAATAAVSASKTTS  491 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~-i~~~------------~~~~-~~~g~afV~F~t~~~A~~Al~~l~~~~  491 (676)
                      ..|.|-+.|... ...|.+.|++||.|..-. ....            +... ...++..|+|.++.+|.+||.. |   
T Consensus         8 ~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-N---   82 (132)
T 3p3d_A            8 LAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-N---   82 (132)
T ss_dssp             CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-T---
T ss_pred             eEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-C---
Confidence            578889997655 457889999999987621 1100            0000 1256789999999999999954 7   


Q ss_pred             CCCeeecCcEEEEEEcc
Q 005812          492 GLGIFLKGRQLTVLKAL  508 (676)
Q Consensus       492 ~~g~~l~gr~l~v~~a~  508 (676)
                        |..|+|..|-|.+..
T Consensus        83 --G~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           83 --GAVFNGVLLGVIPYT   97 (132)
T ss_dssp             --TCEETTEECEEEECC
T ss_pred             --CeEeCcEEEEEEECC
Confidence              899999988888874

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.85  E-value=0.045  Score=57.89  Aligned_cols=56  Identities=21%  Similarity=0.239  Sum_probs=42.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHH
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK  277 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~  277 (676)
                      .++|+|. .|..+++.+|.++|++||.|.++.+-.+     ..-||.|+|.+.+++..++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~-----~g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES-----FGLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS-----SSEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc-----CCeEEEEEeCCHHHHHHHHhc
Confidence            3689997 7999999999999999999999988764     347999999999999977664

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.37  E-value=0.071  Score=56.42  Aligned_cols=55  Identities=15%  Similarity=0.190  Sum_probs=40.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA  486 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~  486 (676)
                      ++|+|. .|..+++.+|.++|++||+|.++...  +..   .-||.|+|.+.+++..++..
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~--~~~---g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFY--ESF---GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEE--CSS---SEEEEEECC---CCHHHHSS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEE--ccC---CeEEEEEeCCHHHHHHHHhc
Confidence            799997 79999999999999999999997443  222   37999999999998877643

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=81.01  E-value=2.9  Score=44.98  Aligned_cols=57  Identities=23%  Similarity=0.300  Sum_probs=46.6

Q ss_pred             eEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCCC
Q 005812          579 RLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNNP  658 (676)
Q Consensus       579 ~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~~  658 (676)
                      .++|. +|..+...+|.++|+         .||.| .|+++             +...|||.|.+++.|..++++++.+|
T Consensus       442 vl~v~-f~~~~~~~~i~~~fs---------~fg~v-~V~wi-------------ddt~a~V~~~~~~~a~~~l~~~~~~~  497 (507)
T 3d45_A          442 VLHVT-FPKEWKTSDLYQLFS---------AFGNI-QISWI-------------DDTSAFVSLSQPEQVQIAVNTSKYAE  497 (507)
T ss_dssp             EEEEE-CCTTCCHHHHHHHGG---------GGCCC-EEEEC-------------SSSEEEEECSCHHHHHHHHHHHTTCS
T ss_pred             EEEEe-CCCCCCHHHHHHHHH---------hcCCE-EEEEE-------------cCCeEEEEECCHHHHHHHHHHHHhCC
Confidence            45555 999999999999998         58865 36655             34579999999999999999998766


Q ss_pred             C
Q 005812          659 S  659 (676)
Q Consensus       659 ~  659 (676)
                      .
T Consensus       498 ~  498 (507)
T 3d45_A          498 S  498 (507)
T ss_dssp             S
T ss_pred             c
Confidence            4

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	676
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-17
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-05
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-16
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-04
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	0.004
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-16
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	0.002
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-16
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-11
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-06
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-04
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-15
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	7e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-04
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	9e-12
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	0.001
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-15
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-09
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-15
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-04
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	8e-15
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-06
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	8e-15
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	0.001
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-14
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	7e-05
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-14
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-07
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	6e-04
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-14
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-10
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-06
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-04
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-10
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	0.001
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-14
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	6e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-05
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-04
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-14
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	0.004
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-14
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	8e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	6e-04
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-14
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-05
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-14
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-05
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	8e-14
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-12
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-08
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	0.002
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	9e-14
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-08
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	0.002
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	9e-14
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	8e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	0.002
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-13
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	8e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-05
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-13
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	9e-10
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	0.003
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-13
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-05
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-13
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-05
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-13
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-08
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-09
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-12
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-12
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	5e-12
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	7e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-05
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	6e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-11
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-04
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	8e-12
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	0.003
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	9e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	0.004
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-11
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-11
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-04
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-05
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	4e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	0.002
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-10
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-10
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	0.004
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-11
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	5e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	0.004
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-11
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-07
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	4e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	9e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-11
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	8e-11
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	6e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-11
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-08
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	8e-11
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	7e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-04
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	8e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-04
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-10
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.001
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-10
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-10
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.004
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-04
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-10
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-10
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	8e-07
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	0.001
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	4e-10
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	4e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	8e-10
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	4e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	9e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	0.001
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-05
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 3e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	4e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	5e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-04
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-08
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	6e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	8e-08
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-08
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-05
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	3e-07
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	3e-06
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	3e-07
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	4e-05
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	6e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-06
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	4e-04
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	2e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	4e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	3e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	1e-05
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	3e-05
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	0.002
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	4e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	7e-05
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	0.001
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-04
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	7e-04

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.0 bits (184), Expect = 2e-17
 Identities = 18/76 (23%), Positives = 35/76 (46%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L + ++        + + FSP G + ++ +  +  T  S G+A+V F    DAE A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 278 FNGQKFGKRPIAVDWA 293
            N      +P+ + W+
Sbjct: 62  MNFDVIKGKPVRIMWS 77

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.9 bits (145), Expect = 5e-12
 Identities = 14/81 (17%), Positives = 37/81 (45%), Gaps = 5/81 (6%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           ++++ +L  D+    + ++FS  G ++S       +T+R  G  ++ F+    A  A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 487 SKTTSGLGIFLKGRQLTVLKA 507
                     +KG+ + ++ +
Sbjct: 62  MN-----FDVIKGKPVRIMWS 77

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.3 bits (94), Expect = 4e-05
 Identities = 10/46 (21%), Positives = 20/46 (43%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          +     +    G+ YV F    DA RA++  N   + G+ + +  +
Sbjct: 32 VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS 77

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 72.3 bits (177), Expect = 2e-16
 Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 2/85 (2%)

Query: 211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRD 270
           G   +   L + N+P     +++  +F   G +    I  +  TG  +G AFV++  + +
Sbjct: 1   GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 60

Query: 271 AESAIQKFNGQKF--GKRPIAVDWA 293
           A+ AI   N      G +P++V  A
Sbjct: 61  AQEAISALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 60.4 bits (146), Expect = 4e-12
 Identities = 19/88 (21%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 420 GEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
           GE      +++ NLP  + ++++   F  +G +V    +  ++T RP+G  F+++   E 
Sbjct: 1   GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 60

Query: 480 ATAAVSASKTTSGLGIFLKGRQLTVLKA 507
           A  A+      + +      + L+V  A
Sbjct: 61  AQEAI---SALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 15/82 (18%)

Query: 575 VSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSR 634
           +  T L + NLP+++T+  L  +                 +   +      +       R
Sbjct: 4   IKDTNLYVTNLPRTITDDQLDTIF---------------GKYGSIVQKNILRDKLTGRPR 48

Query: 635 GVAFVEFTEHQHALVALRVLNN 656
           GVAFV + + + A  A+  LNN
Sbjct: 49  GVAFVRYNKREEAQEAISALNN 70

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 2/42 (4%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSV--GGRKIGVKHA 46
          +   RG  +V++   E+A  A+   N      G + + V+ A
Sbjct: 44 TGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 85

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 72.0 bits (176), Expect = 3e-16
 Identities = 24/78 (30%), Positives = 39/78 (50%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            LI+  +P      E+  +F  +G +    I  +  TG S G+AFV FT + D++ AI+ 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 278 FNGQKFGKRPIAVDWAVP 295
            NG     + + V +A P
Sbjct: 64  LNGITVRNKRLKVSYARP 81

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 56.2 bits (135), Expect = 1e-10
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 5/81 (6%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            + +  LP D+ + E+   F A G + +   +    T    G  F+ F +   +  A+  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 487 SKTTSGLGIFLKGRQLTVLKA 507
                  GI ++ ++L V  A
Sbjct: 64  LN-----GITVRNKRLKVSYA 79

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 11/46 (23%), Positives = 25/46 (54%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          ++    +    G+ +V F    D+ RA+++ NG +V  +++ V +A
Sbjct: 34 IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA 79

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 71.9 bits (176), Expect = 4e-16
 Identities = 29/86 (33%), Positives = 46/86 (53%), Gaps = 2/86 (2%)

Query: 213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTD-TGLSKGFAFVKFTCKRDA 271
           K    K+++RNIPF+A   EI+++FS  G +  V +P     TG  +GF FV F  K+DA
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 272 ESAIQKF-NGQKFGKRPIAVDWAVPK 296
           + A     +      R + ++WA  +
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADSE 90

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.4 bits (141), Expect = 2e-11
 Identities = 25/92 (27%), Positives = 44/92 (47%), Gaps = 5/92 (5%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVS-FVPVLHQVTKRPKGTGFLKFKTVEA 479
           + +  + I + N+PF  +  E+++ FS FGE+ +  +P     T   +G GF+ F T + 
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 63

Query: 480 ATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           A  A +A          L GR+L +  A  + 
Sbjct: 64  AKKAFNALCH----STHLYGRRLVLEWADSEV 91

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.4 bits (102), Expect = 5e-06
 Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVE-MKNGTSVGGRKIGVKHAMHRASLE 53
               G+  HRGFG+V F   +DA +A   + + T + GR++ ++ A    +++
Sbjct: 41 PKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 14/82 (17%)

Query: 576 SRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRG 635
           + +++++ N+P    ++ +++L      S   + K V    K                RG
Sbjct: 7   TTSKILVRNIPFQANQREIRELF-----STFGELKTVRLPKKM---------TGTGAHRG 52

Query: 636 VAFVEFTEHQHALVALRVLNNN 657
             FV+F   Q A  A   L ++
Sbjct: 53  FGFVDFITKQDAKKAFNALCHS 74

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.0 bits (168), Expect = 3e-15
 Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 3/84 (3%)

Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDA 271
           SKT    LI+  +P      E + +F  +G + +  +  +  TG S G+ FV +   +DA
Sbjct: 1   SKT---NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDA 57

Query: 272 ESAIQKFNGQKFGKRPIAVDWAVP 295
           E AI   NG +   + I V +A P
Sbjct: 58  EKAINTLNGLRLQTKTIKVSYARP 81

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 7e-10
 Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 5/83 (6%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           +  + +  LP ++  EE +  F + GE+ S   V  ++T +  G GF+ +   + A  A+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 485 SASKTTSGLGIFLKGRQLTVLKA 507
           +        G+ L+ + + V  A
Sbjct: 62  NTLN-----GLRLQTKTIKVSYA 79

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 5e-04
 Identities = 11/40 (27%), Positives = 22/40 (55%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          + +  G+G+V +   +DA +A+   NG  +  + I V +A
Sbjct: 40 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA 79

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

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]

 Score = 69.3 bits (169), Expect = 3e-15
 Identities = 24/90 (26%), Positives = 43/90 (47%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G    + Q   + +  +  K     + ++F   G V N ++P +  TG  +G+ FV+F  
Sbjct: 1   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 60

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKN 297
           + DA+ AI+  +  K   +PI V+ A   N
Sbjct: 61  EEDADYAIKIMDMIKLYGKPIRVNKASAHN 90

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

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]

 Score = 59.7 bits (144), Expect = 9e-12
 Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 5/91 (5%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
           E     T+++  L   +    + + F   G VV+      +VT + +G GF++F + E A
Sbjct: 5   ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 64

Query: 481 TAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
             A+          I L G+ + V KA    
Sbjct: 65  DYAIKIMD-----MIKLYGKPIRVNKASAHN 90

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

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]

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 13/40 (32%), Positives = 26/40 (65%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          + +H+G+G+V+F   EDA+ A+++ +   + G+ I V  A
Sbjct: 47 TGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA 86

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.2 bits (169), Expect = 4e-15
 Identities = 21/82 (25%), Positives = 39/82 (47%)

Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           +   L + N+ F     +I ++FS  G +  + +  +     + GF FV++  + DAE+A
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 275 IQKFNGQKFGKRPIAVDWAVPK 296
           ++  NG +   R I  DW    
Sbjct: 66  MRYINGTRLDDRIIRTDWDAGF 87

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.8 bits (129), Expect = 1e-09
 Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
            T+++ NL F    E++ + FS  G++   +  L ++ K   G  F+++ +   A  A+ 
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 486 ASKTTSGLGIFLKGRQLTV 504
                   G  L  R +  
Sbjct: 68  YIN-----GTRLDDRIIRT 81

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.4 bits (89), Expect = 2e-04
 Identities = 13/46 (28%), Positives = 18/46 (39%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          M   K      GF +V++    DA  A+   NGT +  R I     
Sbjct: 39 MGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD 84

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 69.4 bits (169), Expect = 4e-15
 Identities = 29/100 (29%), Positives = 49/100 (49%), Gaps = 4/100 (4%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G  GS     +L +RN+ + +   +++ +FS  G +  ++ P ++ T   KGFAFV F  
Sbjct: 4   GSSGSG----RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMF 59

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGAAAG 307
              A  A  + +GQ F  R + V  +  K   S  G ++G
Sbjct: 60  PEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.5 bits (120), Expect = 1e-08
 Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 5/86 (5%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             +F+ NL +    E++++ FSA+G +      +  +TK+PKG  F+ F   E A  A +
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKK 511
                   G   +GR L VL +  KK
Sbjct: 69  EVD-----GQVFQGRMLHVLPSTIKK 89

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.2 bits (88), Expect = 3e-04
 Identities = 12/55 (21%), Positives = 21/55 (38%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQR 55
                + + +GF +V F   E A +A    +G    GR + V  +  +    Q 
Sbjct: 40 YPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQS 94

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.1 bits (166), Expect = 8e-15
 Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 6/88 (6%)

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
           GE + TQ+ +L + N+P      E++ +F   G    V+I  +        F F++   +
Sbjct: 1   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETR 54

Query: 269 RDAESAIQKFNGQKFGKRPIAVDWAVPK 296
             AE A  + +      + + V +A   
Sbjct: 55  TLAEIAKVELDNMPLRGKQLRVRFACHS 82

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.6 bits (105), Expect = 1e-06
 Identities = 12/43 (27%), Positives = 22/43 (51%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASL 52
           +GFG+++      A  A    +   + G+++ V+ A H ASL
Sbjct: 43 DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASL 85

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.2 bits (104), Expect = 2e-06
 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 11/82 (13%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           + +F+ NLP D+  EE+++ F  +G+         +        GF++ +T   A  A  
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKV 62

Query: 486 ASKTTSGLGIFLKGRQLTVLKA 507
                    + L+G+QL V  A
Sbjct: 63  ELD-----NMPLRGKQLRVRFA 79

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 67.8 bits (165), Expect = 8e-15
 Identities = 25/83 (30%), Positives = 46/83 (55%)

Query: 214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAES 273
            + W L + +I  +A+ +EI++ F   G + N+++  +  TG SKG+A V++   + A +
Sbjct: 5   VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 64

Query: 274 AIQKFNGQKFGKRPIAVDWAVPK 296
           A +  NG +   + I VDW   K
Sbjct: 65  AKEALNGAEIMGQTIQVDWCFVK 87

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 49.3 bits (117), Expect = 3e-08
 Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 5/85 (5%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             +F+ ++  +   +E++++F  +GE+ +    L + T   KG   ++++T + A AA  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDK 510
           A       G  + G+ + V     K
Sbjct: 68  ALN-----GAEIMGQTIQVDWCFVK 87

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 10/49 (20%), Positives = 21/49 (42%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
          +   + +   +G+  V++   + A  A E  NG  + G+ I V     +
Sbjct: 39 LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 87

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

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]

 Score = 67.5 bits (164), Expect = 1e-14
 Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVY-IPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           + I N+  +     + D FS  G++     I  + DTG SKG+AF+ F     +++AI+ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 278 FNGQKFGKRPIAVDWAVPKN 297
            NGQ    RPI V +A  K+
Sbjct: 61  MNGQYLCNRPITVSYAFKKD 80

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

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]

 Score = 58.6 bits (141), Expect = 1e-11
 Identities = 27/85 (31%), Positives = 41/85 (48%), Gaps = 6/85 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPV-LHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           IFI NL  ++D + +   FSAFG ++    +     T   KG  F+ F + +A+ AA+ A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 487 SKTTSGLGIFLKGRQLTVLKALDKK 511
                  G +L  R +TV  A  K 
Sbjct: 61  MN-----GQYLCNRPITVSYAFKKD 80

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

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]

 Score = 39.7 bits (92), Expect = 7e-05
 Identities = 12/51 (23%), Positives = 26/51 (50%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRAS 51
          ++    +   +G+ ++ FA  + ++ A+E  NG  +  R I V +A  + S
Sbjct: 31 IMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDS 81

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.8 bits (165), Expect = 1e-14
 Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 2/89 (2%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G   SK+   +L + NIPF+ +  +++ MF   G + +V      +   SKGF FV F  
Sbjct: 3   GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE--IIFNERGSKGFGFVTFEN 60

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPK 296
             DA+ A +K +G     R I V+ A  +
Sbjct: 61  SADADRAREKLHGTVVEGRKIEVNNATAR 89

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 1e-07
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 7/85 (8%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + + N+PF   + +++Q F  FG+++          +  KG GF+ F+    A  A  
Sbjct: 12  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEI--IFNERGSKGFGFVTFENSADADRARE 69

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDK 510
                   G  ++GR++ V  A  +
Sbjct: 70  KLH-----GTVVEGRKIEVNNATAR 89

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 6e-04
 Identities = 20/41 (48%), Positives = 25/41 (60%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRA 50
           +GFG+V F    DA+RA E  +GT V GRKI V +A  R 
Sbjct: 50 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV 90

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.3 bits (164), Expect = 1e-14
 Identities = 21/80 (26%), Positives = 39/80 (48%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL I  +P     +++K++ +  G +    +  ++ TGLSKG+AF ++      + AI  
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 278 FNGQKFGKRPIAVDWAVPKN 297
            NG + G + + V  A    
Sbjct: 63  LNGMQLGDKKLLVQRASVGA 82

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 3e-10
 Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 5/82 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           + +FI  LP  L++++VK+  ++FG + +F  V    T   KG  F ++  +     A++
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 486 ASKTTSGLGIFLKGRQLTVLKA 507
                   G+ L  ++L V +A
Sbjct: 62  GLN-----GMQLGDKKLLVQRA 78

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (100), Expect = 6e-06
 Identities = 10/50 (20%), Positives = 25/50 (50%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRA 50
          +V    +   +G+ + ++  +   ++A+   NG  +G +K+ V+ A   A
Sbjct: 33 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA 82

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (86), Expect = 5e-04
 Identities = 16/78 (20%), Positives = 27/78 (34%), Gaps = 15/78 (19%)

Query: 579 RLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAF 638
           +L I  LP  + +  +K+L                     L++    K      S+G AF
Sbjct: 3   KLFIGGLPNYLNDDQVKELL---------------TSFGPLKAFNLVKDSATGLSKGYAF 47

Query: 639 VEFTEHQHALVALRVLNN 656
            E+ +      A+  LN 
Sbjct: 48  CEYVDINVTDQAIAGLNG 65

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.4 bits (164), Expect = 1e-14
 Identities = 26/85 (30%), Positives = 40/85 (47%)

Query: 214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAES 273
           T K  L +  +  +     +   F P G + ++ IP + +T   +GFAFV+F    DA +
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 274 AIQKFNGQKFGKRPIAVDWAVPKNI 298
           AI   N  +   R I V+ A P  I
Sbjct: 63  AIDNMNESELFGRTIRVNLAKPMRI 87

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 1e-10
 Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 5/87 (5%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           +  +++  L  ++D++ +   F  FG++      L   T++ +G  F++F+  E A AA+
Sbjct: 5   KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64

Query: 485 SASKTTSGLGIFLKGRQLTVLKALDKK 511
                       L GR + V  A   +
Sbjct: 65  DNMN-----ESELFGRTIRVNLAKPMR 86

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 16/40 (40%), Positives = 25/40 (62%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          + +HRGF +V+F + EDA  A++  N + + GR I V  A
Sbjct: 43 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 82

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.4 bits (164), Expect = 1e-14
 Identities = 25/84 (29%), Positives = 36/84 (42%), Gaps = 4/84 (4%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWN--VYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           +L I  IP   K  EI +  + V       +      D   ++GFAFV++   R A  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 276 QKFNGQKF--GKRPIAVDWAVPKN 297
           +K    +       IAVDWA P+ 
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEI 86

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 6e-10
 Identities = 19/96 (19%), Positives = 37/96 (38%), Gaps = 5/96 (5%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFV--PVLHQVTKRPKGTGFLKFKTVEAATAAV 484
            +FI  +P     EE+ +  +   E V  V          + +G  F+++++  AA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 485 SASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDK 520
              +      I L G Q+ V  A  +    +  ++ 
Sbjct: 63  ---RKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 1e-05
 Identities = 19/84 (22%), Positives = 31/84 (36%), Gaps = 13/84 (15%)

Query: 578 TRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVA 637
            RL I  +PK    + + +          +K    +  +             K  +RG A
Sbjct: 2   CRLFIGGIPKMKKREEILEEI--------AKVTEGVLDVIVYA-----SAADKMKNRGFA 48

Query: 638 FVEFTEHQHALVALRVLNNNPSKL 661
           FVE+  H+ A +A R L     +L
Sbjct: 49  FVEYESHRAAAMARRKLMPGRIQL 72

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 3e-04
 Identities = 13/62 (20%), Positives = 22/62 (35%), Gaps = 3/62 (4%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVE--MKNGTSVGGRKIGVKHAMHRASL-EQRRS 57
            +     ++RGF +V++     A  A    M     + G +I V  A     + E    
Sbjct: 35 YASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVME 94

Query: 58 KV 59
           V
Sbjct: 95 TV 96

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.4 bits (164), Expect = 2e-14
 Identities = 26/90 (28%), Positives = 42/90 (46%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G +    +   L I ++P +    ++  MF P G V +  +  +  T LSK F FV +  
Sbjct: 10  GSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN 69

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKN 297
              A++AIQ  NG + G + + V     KN
Sbjct: 70  PVSAQAAIQSMNGFQIGMKRLKVQLKRSKN 99

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 1e-08
 Identities = 26/105 (24%), Positives = 47/105 (44%), Gaps = 7/105 (6%)

Query: 407 SSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRP 466
           + +S   +  Q EG +     +FI +LP +  ++++ Q F  FG VVS    + + T   
Sbjct: 2   TQQSIGAAGSQKEGPEG--ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS 59

Query: 467 KGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           K  GF+ +    +A AA+ +       G  +  ++L V     K 
Sbjct: 60  KCFGFVSYDNPVSAQAAIQSMN-----GFQIGMKRLKVQLKRSKN 99

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (80), Expect = 0.004
 Identities = 10/39 (25%), Positives = 20/39 (51%)

Query: 8  NEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          N  + FG+V +     A  A++  NG  +G +++ V+  
Sbjct: 57 NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK 95

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 66.6 bits (162), Expect = 2e-14
 Identities = 19/86 (22%), Positives = 36/86 (41%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G    K     + ++N+PF   ++EI D F    ++         + G+  G A V F  
Sbjct: 1   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 60

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWA 293
           + +A +A+   N +  G R + +   
Sbjct: 61  RDEATAAVIDLNDRPIGSRKVKLVLG 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.1 bits (114), Expect = 8e-08
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             I + N+PF +  +E+   F  +  +   V + +     P G   + F++ + ATAAV 
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 486 ASKTTSGLGIFLKGRQLTVLKA 507
                      +  R++ ++  
Sbjct: 70  DLN-----DRPIGSRKVKLVLG 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.2 bits (96), Expect = 2e-05
 Identities = 10/46 (21%), Positives = 16/46 (34%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           +         G   V F   ++A  AV   N   +G RK+ +   
Sbjct: 41 CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.0 bits (85), Expect = 6e-04
 Identities = 15/81 (18%), Positives = 25/81 (30%), Gaps = 15/81 (18%)

Query: 576 SRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRG 635
             T + + N+P +++   +        V   S                  K + K    G
Sbjct: 8   GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSV---------------CLKYNEKGMPTG 52

Query: 636 VAFVEFTEHQHALVALRVLNN 656
            A V F     A  A+  LN+
Sbjct: 53  EAMVAFESRDEATAAVIDLND 73

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 65.8 bits (160), Expect = 5e-14
 Identities = 19/79 (24%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L+ +N+ F    +E+K++F     +  V        G SKG A+++F  + DAE  +++
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 278 FNGQKFGKRPIAVDWAVPK 296
             G +   R +++ +   K
Sbjct: 73  KQGAEIDGRSVSLYYTGEK 91

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 46.2 bits (109), Expect = 5e-07
 Identities = 17/86 (19%), Positives = 35/86 (40%), Gaps = 10/86 (11%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
            T+   NL F++  +E+K+ F            L     + KG  +++FK+   A   + 
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKK 511
             +     G  + GR +++    +K 
Sbjct: 72  EKQ-----GAEIDGRSVSLYYTGEKG 92

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 41.6 bits (97), Expect = 2e-05
 Identities = 10/45 (22%), Positives = 21/45 (46%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRAS 51
            + +G  Y++F    DA + +E K G  + GR + + +   +  
Sbjct: 49 DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG 93

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.4 bits (159), Expect = 6e-14
 Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 3/82 (3%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWN---VYIPHNTDTGLSKGFAFVKFTCKRDAESAI 275
           L I+N+ F      +K +FS VG + +       +     LS GF FV++     A+ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 276 QKFNGQKFGKRPIAVDWAVPKN 297
           ++  G       + V  +    
Sbjct: 61  KQLQGHTVDGHKLEVRISERAT 82

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.7 bits (126), Expect = 2e-09
 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 8/83 (9%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQ---VTKRPKGTGFLKFKTVEAATAAV 484
           +FI NL F    E +K  FS  G + S      +         G GF+++K  E A  A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 485 SASKTTSGLGIFLKGRQLTVLKA 507
              +     G  + G +L V  +
Sbjct: 61  KQLQ-----GHTVDGHKLEVRIS 78

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.9 bits (98), Expect = 1e-05
 Identities = 13/41 (31%), Positives = 23/41 (56%)

Query: 6  GSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          G     GFG+V++   E A +A++   G +V G K+ V+ +
Sbjct: 38 GVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS 78

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.8 bits (160), Expect = 8e-14
 Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L IRN+P+K    E+ D+F   G +  + + +      ++G A+V +    DA++A   
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDH 65

Query: 278 FNGQKFGKRPIAVDWAVPK 296
            +G     R + V +    
Sbjct: 66  LSGFNVCNRYLVVLYYNAN 84

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.3 bits (151), Expect = 1e-12
 Identities = 21/110 (19%), Positives = 41/110 (37%), Gaps = 8/110 (7%)

Query: 423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATA 482
           E+   ++I NLP+ +  EE+   F  +G +          T   +GT ++ ++ +  A  
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKN 61

Query: 483 AVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRNLY 532
           A          G  +  R L VL     +     +  K + +    +  Y
Sbjct: 62  ACDHLS-----GFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKY 106

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 4e-08
 Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 8   NEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSKVTQEVQAED 67
            E RG  YV +  + DA  A +  +G +V  R + V +     + ++  +K  +E Q + 
Sbjct: 43  PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEE-QLKL 101

Query: 68  IEK 70
           +++
Sbjct: 102 LKE 104

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 19/82 (23%)

Query: 575 VSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSR 634
           V+R  L I NLP  +T + +  +          K  P+          ++ +V     +R
Sbjct: 6   VNRI-LYIRNLPYKITAEEMYDIF--------GKYGPI----------RQIRVGNTPETR 46

Query: 635 GVAFVEFTEHQHALVALRVLNN 656
           G A+V + +   A  A   L+ 
Sbjct: 47  GTAYVVYEDIFDAKNACDHLSG 68

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.1 bits (158), Expect = 9e-14
 Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 2/84 (2%)

Query: 213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAE 272
           K+    + I+N+        + D FS  G + +  +  + +   SKG+ FV F  +  AE
Sbjct: 5   KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAE 62

Query: 273 SAIQKFNGQKFGKRPIAVDWAVPK 296
            AI+K NG     R + V     +
Sbjct: 63  RAIEKMNGMLLNDRKVFVGRFKSR 86

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 4e-08
 Identities = 28/86 (32%), Positives = 42/86 (48%), Gaps = 7/86 (8%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             IFI NL   +DN+ +   FSAFG ++S    +       KG GF+ F+T EAA  A+ 
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSC--KVVCDENGSKGYGFVHFETQEAAERAIE 66

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKK 511
                   G+ L  R++ V +   +K
Sbjct: 67  KMN-----GMLLNDRKVFVGRFKSRK 87

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 15/40 (37%), Positives = 21/40 (52%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
           +G+G+V F   E A RA+E  NG  +  RK+ V     R
Sbjct: 47 SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 86

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

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

 Score = 65.1 bits (158), Expect = 9e-14
 Identities = 23/80 (28%), Positives = 42/80 (52%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            + + N+    +  +++++F P G +  +Y+  +  TG SKGFAF+ F  + DA  AI  
Sbjct: 10  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 69

Query: 278 FNGQKFGKRPIAVDWAVPKN 297
            +G  +    + V+WA P  
Sbjct: 70  VSGFGYDHLILNVEWAKPST 89

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

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

 Score = 53.9 bits (129), Expect = 8e-10
 Identities = 20/82 (24%), Positives = 31/82 (37%), Gaps = 5/82 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
            TI + NL  D    ++++ F  FG +        + T + KG  F+ F   E A  A++
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 486 ASKTTSGLGIFLKGRQLTVLKA 507
                   G       L V  A
Sbjct: 69  GVS-----GFGYDHLILNVEWA 85

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 12/46 (26%), Positives = 22/46 (47%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          +   K + + +GF ++ F   EDA RA+   +G       + V+ A
Sbjct: 40 LAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA 85

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.7 bits (157), Expect = 2e-13
 Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           Q  KL I  + F+     +++ +   G + +  +  +  +  S+GF FV F+   + ++A
Sbjct: 19  QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 78

Query: 275 IQKFNGQKFGKRPIAVDWAVPK 296
           +          R +    AV +
Sbjct: 79  M-AARPHSIDGRVVEPKRAVAR 99

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.1 bits (145), Expect = 8e-12
 Identities = 23/105 (21%), Positives = 51/105 (48%), Gaps = 8/105 (7%)

Query: 407 SSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRP 466
           + ++ P  L++ + E E    +FI  L F+   E ++  +  +G++   V +    +KR 
Sbjct: 4   TLETVP--LERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRS 61

Query: 467 KGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           +G GF+ F ++    AA++A          + GR +   +A+ ++
Sbjct: 62  RGFGFVTFSSMAEVDAAMAA------RPHSIDGRVVEPKRAVARE 100

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.6 bits (97), Expect = 2e-05
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
          ++    S   RGFG+V F+ M + + A+      S+ GR +  K A+ R
Sbjct: 52 VMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAR 99

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.9 bits (155), Expect = 2e-13
 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L +  +P      E++ +FS  G +    I  +  TG+S+G  F++F  + +AE AI+ 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 278 FNGQKFG--KRPIAVDWA 293
            NGQK      PI V +A
Sbjct: 68  LNGQKPSGATEPITVKFA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 9e-10
 Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 3/81 (3%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            +++  LP  +  +E++Q FS +G +++   ++ QVT   +G GF++F     A  A+  
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI-- 65

Query: 487 SKTTSGLGIFLKGRQLTVLKA 507
            K  +G         +TV  A
Sbjct: 66  -KGLNGQKPSGATEPITVKFA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 0.003
 Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 15/79 (18%)

Query: 578 TRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVA 637
             L +  LPK+MT+K L++L                 Q   + + +         SRGV 
Sbjct: 7   ANLYVSGLPKTMTQKELEQLF---------------SQYGRIITSRILVDQVTGVSRGVG 51

Query: 638 FVEFTEHQHALVALRVLNN 656
           F+ F +   A  A++ LN 
Sbjct: 52  FIRFDKRIEAEEAIKGLNG 70

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 63.5 bits (154), Expect = 2e-13
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ I  + ++     +++ F   G V    +  +  T  S+GF FV F  +   +  + +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 278 FNGQKFGKRPIAVDWA 293
            +  +   + I    A
Sbjct: 62  -SRHELDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.8 bits (147), Expect = 2e-12
 Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +FI  L +    E +++ F  FGEV   + +   +TKR +G GF+ F         ++ S
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 488 KTTSGLGIFLKGRQLTVLKA 507
           +        L  + +    A
Sbjct: 63  RHE------LDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.1 bits (96), Expect = 2e-05
 Identities = 9/46 (19%), Positives = 19/46 (41%), Gaps = 1/46 (2%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          ++    +   RGFG+V F      ++ +   +   +  + I  K A
Sbjct: 32 VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTIDPKVA 76

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 63.0 bits (153), Expect = 3e-13
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL++ N+ F     +I+++F+  G +    + ++  +G S G A V F  K DA  A+++
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 60

Query: 278 FNGQKFGKRPIAVDWA 293
           +NG     RP+ +   
Sbjct: 61  YNGVPLDGRPMNIQLV 76

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.0 bits (127), Expect = 1e-09
 Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 6/77 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           + + NL F + + ++++ F+ FG +     V +  + R  GT  + F+    A  A+   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKK-AAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 488 KTTSGLGIFLKGRQLTV 504
                 G+ L GR + +
Sbjct: 62  N-----GVPLDGRPMNI 73

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (92), Expect = 7e-05
 Identities = 12/46 (26%), Positives = 19/46 (41%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           V    S    G   V F    DA +A++  NG  + GR + ++  
Sbjct: 31 AVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 76

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.6 bits (152), Expect = 8e-13
 Identities = 18/88 (20%), Positives = 42/88 (47%), Gaps = 9/88 (10%)

Query: 218 KLIIRNI-PFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ 276
           ++ I N+     K ++++ +FS  G +    +          GFAFV++  +R+A +A+ 
Sbjct: 17  RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNARAAVA 68

Query: 277 KFNGQKFGKRPIAVDWAVPKNIYSSGGA 304
             +G+    + + ++ A    +  SG +
Sbjct: 69  GEDGRMIAGQVLDINLAAEPKVNRSGPS 96

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.5 bits (118), Expect = 3e-08
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 14/92 (15%)

Query: 421 EDELQNTIFICNL-PFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
              + + +FI NL    +   +V+  FS +G++V             KG  F+++     
Sbjct: 11  PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVG--------CSVHKGFAFVQYVNERN 62

Query: 480 ATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           A AAV+        G  + G+ L +  A + K
Sbjct: 63  ARAAVAGED-----GRMIAGQVLDINLAAEPK 89

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 11/37 (29%), Positives = 21/37 (56%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          H+GF +VQ+    +A  AV  ++G  + G+ + +  A
Sbjct: 49 HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA 85

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.3 bits (155), Expect = 2e-12
 Identities = 28/177 (15%), Positives = 50/177 (28%), Gaps = 5/177 (2%)

Query: 121 ARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYT 180
            R + IGGL      E +       GT+               G                
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 181 TVKSACASVALLHQKEIKGGTVWARQLGGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPV 240
             +       ++  K         R     G+     K+ +  I    + + ++D F   
Sbjct: 66  NARPHKVDGRVVEPKRAVSREDSQRP----GAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 121

Query: 241 GLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKN 297
           G +  + I  +  +G  +GFAFV F      +  + +            V  A+ K 
Sbjct: 122 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQ 177

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (133), Expect = 2e-09
 Identities = 22/66 (33%), Positives = 35/66 (53%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
           E E    +FI  L F+  +E ++  F  +G +   V +    TKR +G GF+ + TVE  
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61

Query: 481 TAAVSA 486
            AA++A
Sbjct: 62  DAAMNA 67

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.8 bits (115), Expect = 3e-07
 Identities = 14/69 (20%), Positives = 30/69 (43%)

Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           Q  KL I  + F+     ++  F   G + +  +  + +T  S+GF FV +    + ++A
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 275 IQKFNGQKF 283
           +     +  
Sbjct: 65  MNARPHKVD 73

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (98), Expect = 5e-05
 Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 4/57 (7%)

Query: 1   MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           ++T +GS + RGF +V F   +  ++ V      +V G    V+ A+ +   ++  S
Sbjct: 129 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSK---QEMAS 181

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.9 bits (147), Expect = 2e-12
 Identities = 24/80 (30%), Positives = 38/80 (47%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL +  + F      ++ +FS  G +  V +  + +T  S+GF FV F    DA+ A+  
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 278 FNGQKFGKRPIAVDWAVPKN 297
            NG+    R I VD A   +
Sbjct: 67  MNGKSVDGRQIRVDQAGKSS 86

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 3e-08
 Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 5/87 (5%)

Query: 425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           +  +F+  L FD + + ++Q FS +G++   V V  + T+R +G GF+ F+ ++ A  A+
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 485 SASKTTSGLGIFLKGRQLTVLKALDKK 511
            A       G  + GRQ+ V +A    
Sbjct: 65  MAMN-----GKSVDGRQIRVDQAGKSS 86

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 4e-05
 Identities = 20/51 (39%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          +   RGFG+V F  ++DA  A+   NG SV GR+I V  A         RS
Sbjct: 43 TQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS---SDNRS 90

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

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

 Score = 61.3 bits (148), Expect = 3e-12
 Identities = 23/99 (23%), Positives = 38/99 (38%), Gaps = 4/99 (4%)

Query: 208 GGEGSKTQK---WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVK 264
           G  GS+  K   +   + N+P+      IK+ F  + +         ++    KGF + +
Sbjct: 4   GSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAE 63

Query: 265 FTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGG 303
           F       SA+   N +  G + I VD A       SG 
Sbjct: 64  FEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKDSGP 101

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

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

 Score = 48.2 bits (114), Expect = 1e-07
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 6/90 (6%)

Query: 422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAAT 481
                T F+ NLP+D+  E +K+ F         +P      +R KG G+ +F+ +++  
Sbjct: 12  KSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLL 71

Query: 482 AAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           +A+S +         L  +++ V  A   +
Sbjct: 72  SALSLN------EESLGNKRIRVDVADQAQ 95

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (146), Expect = 5e-12
 Identities = 22/93 (23%), Positives = 36/93 (38%), Gaps = 3/93 (3%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ +  +P+      ++  F   G +    +  +  TG S+G+ FV    +  AE A + 
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSS--GGAAAGV 308
            N      R   V+ A       S   G A GV
Sbjct: 72  PNP-IIDGRKANVNLAYLGAKPRSLQTGFAIGV 103

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (123), Expect = 7e-09
 Identities = 20/91 (21%), Positives = 36/91 (39%), Gaps = 6/91 (6%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
           +D     IF+  LP+   +  +++ F  FG++   V +  + T + +G GF+      AA
Sbjct: 6   KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 65

Query: 481 TAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
             A             + GR+  V  A    
Sbjct: 66  ERACKD------PNPIIDGRKANVNLAYLGA 90

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 4e-05
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          ++T + + + RG+G+V  A    A RA +  N   + GRK  V  A   A     ++
Sbjct: 42 VITDRQTGKSRGYGFVTMADRAAAERACKDPNPI-IDGRKANVNLAYLGAKPRSLQT 97

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.0 bits (145), Expect = 6e-12
 Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 2/79 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            LI+  +P+K    ++K+ FS  G V  V +  +  TG SKGF FV+FT        + +
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 278 FNGQKFGKRPIAVDWAVPK 296
            +      R         K
Sbjct: 70  RH--MIDGRWCDCKLPNSK 86

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 5e-11
 Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 7/86 (8%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           + + +  LP+    +++K+ FS FGEV+         T   KG GF++F   E     +S
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKK 511
                      + GR         K+
Sbjct: 69  QRHM-------IDGRWCDCKLPNSKQ 87

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 10/51 (19%), Positives = 21/51 (41%), Gaps = 2/51 (3%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRAS 51
          +     +   +GFG+V+F   E   + +  ++   + GR    K    + S
Sbjct: 40 VKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHM--IDGRWCDCKLPNSKQS 88

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 8e-12
 Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L + N+        I  +FS +G          T+   +  + FV+F   RDA +A+  
Sbjct: 10  TLYVGNLSRDVTEVLILQLFSQIG--PCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAA 67

Query: 278 FNGQKFGKRPIAVDWAVPKN 297
            NG+K   + + V+WA   +
Sbjct: 68  MNGRKILGKEVKVNWATTPS 87

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 5e-08
 Identities = 22/92 (23%), Positives = 36/92 (39%), Gaps = 8/92 (8%)

Query: 421 EDELQN-TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
           ED+ Q  T+++ NL  D+    + Q FS  G   S                F++F     
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKM--ITEHTSNDPYCFVEFYEHRD 60

Query: 480 ATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           A AA++A       G  + G+++ V  A    
Sbjct: 61  AAAALAAMN-----GRKILGKEVKVNWATTPS 87

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 0.003
 Identities = 10/39 (25%), Positives = 19/39 (48%)

Query: 8  NEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
            +  + +V+F    DA  A+   NG  + G+++ V  A
Sbjct: 45 TSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA 83

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.6 bits (144), Expect = 9e-12
 Identities = 15/85 (17%), Positives = 27/85 (31%), Gaps = 6/85 (7%)

Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDA 271
           S  +   +    I        ++  FSP G +  + +           ++FV+F+    A
Sbjct: 14  SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESA 67

Query: 272 ESAIQKFNGQKFGKRPIAVDWAVPK 296
             AI   NG       +   W    
Sbjct: 68  AHAIVSVNGTTIEGHVVKCYWGKES 92

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 6e-06
 Identities = 19/96 (19%), Positives = 41/96 (42%), Gaps = 12/96 (12%)

Query: 410 SKPKSLKQTEGEDELQN-TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKG 468
           +K    +    +   +N T++   +   L ++ ++Q FS FG+++             KG
Sbjct: 2   TKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEI------RVFPEKG 55

Query: 469 TGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV 504
             F++F T E+A  A+ +       G  ++G  +  
Sbjct: 56  YSFVRFSTHESAAHAIVSVN-----GTTIEGHVVKC 86

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 10/43 (23%), Positives = 20/43 (46%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASL 52
           +G+ +V+F+  E A  A+   NGT++ G  +          +
Sbjct: 53 EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDM 95

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 58.7 bits (141), Expect = 1e-11
 Identities = 18/78 (23%), Positives = 31/78 (39%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L + N P       I+D+   + +V       +     S+ FA++  T K DA   ++K
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 278 FNGQKFGKRPIAVDWAVP 295
            NG K     +    + P
Sbjct: 63  LNGLKIEGYTLVTKVSNP 80

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.8 bits (118), Expect = 2e-08
 Identities = 10/81 (12%), Positives = 25/81 (30%), Gaps = 5/81 (6%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T+++ N P       ++        V   + +        +   ++   + E A   V  
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 487 SKTTSGLGIFLKGRQLTVLKA 507
                  G+ ++G  L    +
Sbjct: 63  LN-----GLKIEGYTLVTKVS 78

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 1e-11
 Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 7/84 (8%)

Query: 218 KLIIRNIPFKAKVNEIK----DMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAES 273
            + I N+  K K +E+K     +FS  G + ++ +  +      +G AFV F     A +
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---MRGQAFVIFKEVSSATN 61

Query: 274 AIQKFNGQKFGKRPIAVDWAVPKN 297
           A++   G  F  +P+ + +A   +
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDS 85

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 1e-07
 Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 6/86 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSA-FGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAV 484
           +TI+I NL   +  +E+K+   A F      + +L   + + +G  F+ FK V +AT A+
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 485 SASKTTSGLGIFLKGRQLTVLKALDK 510
            + +     G     + + +  A   
Sbjct: 64  RSMQ-----GFPFYDKPMRIQYAKTD 84

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.7 bits (87), Expect = 4e-04
 Identities = 8/37 (21%), Positives = 16/37 (43%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           RG  +V F  +  A  A+    G     + + +++A
Sbjct: 45 MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 81

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 1e-11
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 1/80 (1%)

Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           Q  KL I  + F+     ++  F   G + +  +  + +T  S+GF FV +    + ++A
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 275 IQKFNGQKFGKRPIAVDWAV 294
           +      K   R +    AV
Sbjct: 65  M-NARPHKVDGRVVEPKRAV 83

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 2e-11
 Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 6/88 (6%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
           E E    +FI  L F+  +E ++  F  +G +   V +    TKR +G GF+ + TVE  
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61

Query: 481 TAAVSASKTTSGLGIFLKGRQLTVLKAL 508
            AA++A          + GR +   +A+
Sbjct: 62  DAAMNA------RPHKVDGRVVEPKRAV 83

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 4e-05
 Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAM 47
          ++    +   RGFG+V +A +E+ + A+       V GR +  K A+
Sbjct: 38 VMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAV 83

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 2e-11
 Identities = 19/80 (23%), Positives = 32/80 (40%), Gaps = 6/80 (7%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L +RN+        I+  F+ +                 + +AFV F+ + DA  A++ 
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAV------ERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 278 FNGQKFGKRPIAVDWAVPKN 297
            NG+     PI V  A P +
Sbjct: 64  LNGKVLDGSPIEVTLAKPVD 83

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 4e-06
 Identities = 17/85 (20%), Positives = 31/85 (36%), Gaps = 11/85 (12%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            +++ NL      E +++ F+      +  P   +  K+ +   F+ F   E A  A+ A
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFN------NIKPGAVERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 487 SKTTSGLGIFLKGRQLTVLKALDKK 511
                  G  L G  + V  A    
Sbjct: 64  LN-----GKVLDGSPIEVTLAKPVD 83

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 13/46 (28%), Positives = 21/46 (45%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
              +   + R + +V F+  EDA  A++  NG  + G  I V  A
Sbjct: 34 PGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 79

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 2e-11
 Identities = 21/104 (20%), Positives = 45/104 (43%), Gaps = 7/104 (6%)

Query: 409 KSKPKS-LKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPK 467
           KS  +  +     E+    T+F   L   +   +++  FSA G+V     +  + ++R K
Sbjct: 1   KSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 60

Query: 468 GTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           G  +++F  +++   A+  +      G  L G  + V  +  +K
Sbjct: 61  GIAYVEFCEIQSVPLAIGLT------GQRLLGVPIIVQASQAEK 98

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 2e-10
 Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            +    +  + +  +++D FS VG V +V I  + ++  SKG A+V+F   +        
Sbjct: 20  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP-LAIG 78

Query: 278 FNGQKFGKRPIAVDWAVPK 296
             GQ+    PI V  +  +
Sbjct: 79  LTGQRLLGVPIIVQASQAE 97

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 2e-11
 Identities = 22/83 (26%), Positives = 40/83 (48%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G   +      L +  +       +++++FS  G + +V I ++  +  S+GFAFV F  
Sbjct: 1   GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 268 KRDAESAIQKFNGQKFGKRPIAV 290
             DA+ A ++ NG +   R I V
Sbjct: 61  VDDAKEAKERANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 1e-10
 Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + +  L       ++++ FS +G +     V  Q ++R +G  F+ F+ V+ A  A  
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 486 ASKTTSGLGIFLKGRQLTV 504
            +      G+ L GR++ V
Sbjct: 70  RAN-----GMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.7 bits (79), Expect = 0.004
 Identities = 16/37 (43%), Positives = 21/37 (56%)

Query: 7  SNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGV 43
          S   RGF +V F  ++DA  A E  NG  + GR+I V
Sbjct: 47 SRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 59.5 bits (143), Expect = 2e-11
 Identities = 30/135 (22%), Positives = 53/135 (39%), Gaps = 11/135 (8%)

Query: 187 ASVALLHQKEIKGGTVWARQLGGEGSKTQKW-----------KLIIRNIPFKAKVNEIKD 235
           + + L+ Q +  G T   +QL  +  +                L++  IP      +++ 
Sbjct: 2   SQIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQ 61

Query: 236 MFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP 295
           +F   G + +V I  + +T  S+G+ FVKF     A+ AI   NG     + + V  A  
Sbjct: 62  LFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS 121

Query: 296 KNIYSSGGAAAGVQN 310
            +       A G  N
Sbjct: 122 GHQRPGIAGAVGDGN 136

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 50.3 bits (119), Expect = 5e-08
 Identities = 26/131 (19%), Positives = 53/131 (40%), Gaps = 11/131 (8%)

Query: 403 SKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQV 462
            +L   + +     Q   E ++   + +  +P  +D  +++Q F  +G + S   V  + 
Sbjct: 20  QQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE 79

Query: 463 TKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSK 522
           T++ +G GF+KF++  +A  A++        G  +  ++L V       LA         
Sbjct: 80  TRQSRGYGFVKFQSGSSAQQAIAGLN-----GFNILNKRLKV------ALAASGHQRPGI 128

Query: 523 NETNDHRNLYL 533
                  N YL
Sbjct: 129 AGAVGDGNGYL 139

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 36.0 bits (82), Expect = 0.004
 Identities = 11/41 (26%), Positives = 21/41 (51%)

Query: 10  HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRA 50
            RG+G+V+F     A +A+   NG ++  +++ V  A    
Sbjct: 83  SRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH 123

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.4 bits (138), Expect = 3e-11
 Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 7/80 (8%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           KL I N+      ++++ +F    L     +       L  G+AFV +  +  A  AI+ 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV------LLKSGYAFVDYPDQNWAIRAIET 56

Query: 278 FNGQ-KFGKRPIAVDWAVPK 296
            +G+ +   + + VD++V K
Sbjct: 57  LSGKVELHGKIMEVDYSVSK 76

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 3e-07
 Identities = 15/86 (17%), Positives = 32/86 (37%), Gaps = 10/86 (11%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           N ++I NL   +  ++++Q F      ++             G  F+ +     A  A+ 
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKLPLAG------QVLLKSGYAFVDYPDQNWAIRAIE 55

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKK 511
                    + L G+ + V  ++ KK
Sbjct: 56  TLSGK----VELHGKIMEVDYSVSKK 77

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.9 bits (137), Expect = 4e-11
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ +  +       +I++ F   G V ++ +P +  T   +GF F+ F  +   +  ++K
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 278 FNGQKFGKRPIAVDWA 293
                 G     +  A
Sbjct: 61  -KYHNVGLSKCEIKVA 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.1 bits (135), Expect = 9e-11
 Identities = 18/80 (22%), Positives = 31/80 (38%), Gaps = 6/80 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           IF+  L  D   E++++ F  FGEV S    +   T + +G  F+ FK  E     +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 488 KTTSGLGIFLKGRQLTVLKA 507
                    +   +  +  A
Sbjct: 62  YHN------VGLSKCEIKVA 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.4 bits (89), Expect = 2e-04
 Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 1/46 (2%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          +     +N+ RGF ++ F   E   + +E K    VG  K  +K A
Sbjct: 31 LPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHN-VGLSKCEIKVA 75

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 6e-11
 Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 3/79 (3%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++ + N+P   +  +I+D+F   G + ++ + +         FAFV+F   RDAE A+  
Sbjct: 16  RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAEDAVYG 72

Query: 278 FNGQKFGKRPIAVDWAVPK 296
            +G  +    + V++    
Sbjct: 73  RDGYDYDGYRLRVEFPRSG 91

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 2e-07
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 8/82 (9%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             I++ NLP D+  ++++  F  +G +     +  +  +      F++F+    A  AV 
Sbjct: 15  CRIYVGNLPPDIRTKDIEDVFYKYGAI---RDIDLKNRRGGPPFAFVEFEDPRDAEDAVY 71

Query: 486 ASKTTSGLGIFLKGRQLTVLKA 507
                   G    G +L V   
Sbjct: 72  GRD-----GYDYDGYRLRVEFP 88

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 6e-04
 Identities = 11/46 (23%), Positives = 19/46 (41%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           +  K       F +V+F    DA  AV  ++G    G ++ V+  
Sbjct: 43 DIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP 88

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.1 bits (137), Expect = 8e-11
 Identities = 17/79 (21%), Positives = 33/79 (41%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L ++N+  +    ++  +F+         I     TG  +G AF+ F  K  A  A+  
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 278 FNGQKFGKRPIAVDWAVPK 296
            NG K   + + +++   K
Sbjct: 80  VNGYKLYGKILVIEFGKNK 98

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 6e-06
 Identities = 22/103 (21%), Positives = 37/103 (35%), Gaps = 7/103 (6%)

Query: 409 KSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKG 468
           +  P       GE      +++ NL   +   ++   F+ F E          +T R +G
Sbjct: 4   RKIPMFSSYNPGEPN--KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRG 61

Query: 469 TGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
             F+ F   E A  A+         G  L G+ L +    +KK
Sbjct: 62  QAFITFPNKEIAWQALHLVN-----GYKLYGKILVIEFGKNKK 99

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.1 bits (137), Expect = 8e-11
 Identities = 26/79 (32%), Positives = 48/79 (60%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            + + NIP++A   ++KD+FS VG V +  + ++ +TG  KG+ F ++  +  A SA++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 278 FNGQKFGKRPIAVDWAVPK 296
            NG++F  R + VD A  +
Sbjct: 70  LNGREFSGRALRVDNAASE 88

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.6 bits (115), Expect = 8e-08
 Identities = 30/91 (32%), Positives = 46/91 (50%), Gaps = 5/91 (5%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
            D    ++F+ N+P++   E++K  FS  G VVSF  V  + T +PKG GF +++  E A
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 481 TAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
            +A+         G    GR L V  A  +K
Sbjct: 64  LSAMRNLN-----GREFSGRALRVDNAASEK 89

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 2e-05
 Identities = 13/48 (27%), Positives = 24/48 (50%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
           +G+G+ ++   E A  A+   NG    GR + V +A    + E+ +S
Sbjct: 49 PKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKS 96

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.1 bits (137), Expect = 8e-11
 Identities = 20/97 (20%), Positives = 43/97 (44%), Gaps = 8/97 (8%)

Query: 213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLV--------WNVYIPHNTDTGLSKGFAFVK 264
            +    + ++ +     ++++ D F   G+V          ++I  + +TG  KG A V 
Sbjct: 5   DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 265 FTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSS 301
           +     A++A++ F+G+ F    + V  A  K   +S
Sbjct: 65  YEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 101

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.6 bits (115), Expect = 7e-08
 Identities = 22/98 (22%), Positives = 36/98 (36%), Gaps = 13/98 (13%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPV--------LHQVTKRPKGTGFL 472
           ED   + I++  L   +  +++   F   G V              L + T +PKG   +
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 473 KFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
            ++    A AAV         G   +G +L V  A  K
Sbjct: 64  SYEDPPTAKAAVEWFD-----GKDFQGSKLKVSLARKK 96

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 4e-04
 Identities = 12/50 (24%), Positives = 20/50 (40%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRA 50
          +   K + + +G   V +     A  AVE  +G    G K+ V  A  + 
Sbjct: 48 IYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 97

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.5 bits (133), Expect = 2e-10
 Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 1/76 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ +  +     V ++K  F   G V +  +  +  T   +GF FV F  +   E    +
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 278 FNGQKFGKRPIAVDWA 293
            +  +   + +    A
Sbjct: 60  IHFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.6 bits (128), Expect = 8e-10
 Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           IF+  L  +   E+VK  F  FG+V   + +  + T R +G GF+ F++ +         
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 488 KTTSGLGIFLKGRQLTVLKA 507
                    +  + +   KA
Sbjct: 62  ------FHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.0 bits (85), Expect = 5e-04
 Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          ++  K +N HRGFG+V F   +   +  E+ +   +  + +  K A
Sbjct: 31 LMFDKTTNRHRGFGFVTFESEDIVEKVCEI-HFHEINNKMVECKKA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 2e-10
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 6/80 (7%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           +FI  L +D   +++K  FS FGEVV     L  +T R +G GF+ FK  E+    +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 488 KTTSGLGIFLKGRQLTVLKA 507
           +        L G+ +   +A
Sbjct: 62  EHK------LNGKVIDPKRA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 3e-10
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ I  + +     ++KD FS  G V +  +  +  TG S+GF FV F      +  + +
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 278 FNGQKFGKRPIAV 290
               K   + I  
Sbjct: 61  -KEHKLNGKVIDP 72

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 3e-05
 Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 1/46 (2%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
          +     +   RGFG+V F   E  ++ ++      + G+ I  K A
Sbjct: 31 LKLDPITGRSRGFGFVLFKESESVDKVMDQ-KEHKLNGKVIDPKRA 75

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.1 bits (135), Expect = 2e-10
 Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 3/85 (3%)

Query: 220 IIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGL--SKGFAFVKFTCKRDAESAIQK 277
           ++ +  ++  V +++D  S  GLV ++ IP   D       G  FV+FT   D + A+Q 
Sbjct: 18  LLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQG 77

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSG 302
             G+KF  R +   +    + Y   
Sbjct: 78  LTGRKFANRVVVTKYC-DPDSYHRR 101

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 8/41 (19%), Positives = 16/41 (39%)

Query: 6  GSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
                G  +V+F  + D  +A++   G     R +  K+ 
Sbjct: 53 VEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYC 93

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 2e-10
 Identities = 21/90 (23%), Positives = 41/90 (45%), Gaps = 11/90 (12%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFV-----PVLHQVTKRPKGTGFLKFKTVEAAT 481
            +++ N+PF +  E +   F+A   +         PVL     + K   FL+F++V+  T
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 482 AAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
            A++        GI  +G+ L + +  D +
Sbjct: 63  QAMAFD------GIIFQGQSLKIRRPHDYQ 86

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.8 bits (131), Expect = 4e-10
 Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 6/81 (7%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIP-----HNTDTGLSKGFAFVKFTCKRDAE 272
           +L + NIPF      + D F+    +  +                K FAF++F    +  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 273 SAIQKFNGQKFGKRPIAVDWA 293
            A+  F+G  F  + + +   
Sbjct: 63  QAMA-FDGIIFQGQSLKIRRP 82

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (80), Expect = 0.004
 Identities = 7/46 (15%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           V     N+ + F +++F  +++  +A+   +G    G+ + ++  
Sbjct: 38 PVLAVQINQDKNFAFLEFRSVDETTQAMAF-DGIIFQGQSLKIRRP 82

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 2e-10
 Identities = 12/83 (14%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++I+ N+ +   ++ +  +FS  G V  +          ++  A +++     A+ A   
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLS 64

Query: 278 FNGQKF--GKRPIAVDWAVPKNI 298
            +GQ        + +D++   ++
Sbjct: 65  LDGQNIYNACCTLRIDFSKLTSL 87

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 3e-10
 Identities = 20/101 (19%), Positives = 37/101 (36%), Gaps = 7/101 (6%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           I + NL + +  + + Q FS FG V+  +          +    L++    +A  A    
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAK--- 62

Query: 488 KTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDH 528
            +  G  I+     L +  +    L      DKS++ T   
Sbjct: 63  LSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPD 103

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.7 bits (87), Expect = 5e-04
 Identities = 15/89 (16%), Positives = 31/89 (34%), Gaps = 21/89 (23%)

Query: 578 TRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVA 637
            R+++ NL   +T   L ++          K   V+K I F              ++  A
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFS--------KFGTVLKIITF-----------TKNNQFQA 48

Query: 638 FVEFTEHQHALVALRVLNNNPSKLFYHHC 666
            +++ +   A  A   L+     ++   C
Sbjct: 49  LLQYADPVSAQHAKLSLDGQN--IYNACC 75

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.6 bits (133), Expect = 3e-10
 Identities = 26/97 (26%), Positives = 43/97 (44%), Gaps = 1/97 (1%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G          + +R +PF     EI   FS + +V N         G S G AFV+F  
Sbjct: 7   GNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFAS 66

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGA 304
           +  AE A++K + ++ G R I +  +    + +SG +
Sbjct: 67  QEIAEKALKK-HKERIGHRYIEIFKSSRAEVRTSGPS 102

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 2e-05
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + +  LPF    EE+ Q FS    V + + +      R  G  F++F + E A  A+ 
Sbjct: 16  GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK 75

Query: 486 ASKTTSGLGIFLKGRQLTVLKA 507
             K        +  R + + K+
Sbjct: 76  KHKER------IGHRYIEIFKS 91

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.2 bits (132), Expect = 4e-10
 Identities = 17/83 (20%), Positives = 30/83 (36%), Gaps = 1/83 (1%)

Query: 214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAES 273
           + K    I NIPF     ++      + +  N       + G   G A V+F  + DA  
Sbjct: 6   SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 65

Query: 274 AIQKFNGQKFGKRPIAVDWAVPK 296
           + +  + +K   R   V     +
Sbjct: 66  SERL-HRKKLNGREAFVHVVTLE 87

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (107), Expect = 8e-07
 Identities = 19/94 (20%), Positives = 34/94 (36%), Gaps = 7/94 (7%)

Query: 419 EGE-DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTV 477
           EG+ +  +    I N+PF +   +V Q         + V VL     +  G   ++FK  
Sbjct: 1   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 60

Query: 478 EAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           + A  +    +        L GR+  V     + 
Sbjct: 61  DDARKSERLHRKK------LNGREAFVHVVTLED 88

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.7 bits (84), Expect = 0.001
 Identities = 11/58 (18%), Positives = 22/58 (37%), Gaps = 1/58 (1%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRSK 58
           V    + +  G   VQF   +DA ++  + +   + GR+  V         E  ++ 
Sbjct: 40 HVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTLEDMREIEKNP 96

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.8 bits (131), Expect = 4e-10
 Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 6/90 (6%)

Query: 214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAES 273
           T+   + IRN+ F ++   + ++    G +  V +  + DT  SKG AF +F  +  A+ 
Sbjct: 6   TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 274 AIQKFN------GQKFGKRPIAVDWAVPKN 297
            +   +      G K   R + VD AV ++
Sbjct: 66  CLAAASLEAEGGGLKLDGRQLKVDLAVTRD 95

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.4 bits (117), Expect = 4e-08
 Identities = 33/87 (37%), Positives = 46/87 (52%), Gaps = 1/87 (1%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
            T+FI NL FD + E + +    FG++     VLH  T+  KG  F +F T EAA   ++
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 486 A-SKTTSGLGIFLKGRQLTVLKALDKK 511
           A S    G G+ L GRQL V  A+ + 
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLAVTRD 95

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.6 bits (128), Expect = 8e-10
 Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 11/95 (11%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G  GS      ++++N+P  +   E+ D+     L +     +          AFV    
Sbjct: 1   GSSGSS----GILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNK-------RTAFVTLLN 49

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSG 302
              A++AIQ F+   F  + + V       +  SG
Sbjct: 50  GEQAQNAIQMFHQYSFRGKDLIVQLQPTDALLCSG 84

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 4e-04
 Identities = 18/88 (20%), Positives = 28/88 (31%), Gaps = 12/88 (13%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           + I + NLP D + +EV      +          +    R K T F+     E A  A+ 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKKLA 513
                       +G+ L V       L 
Sbjct: 59  MFH-----QYSFRGKDLIVQLQPTDALL 81

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.8 bits (129), Expect = 1e-09
 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 4/69 (5%)

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
            +++   S  G +  + +          G A V F    +A+  IQ  +G+ FG R I  
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

Query: 291 DWAVPKNIY 299
                   Y
Sbjct: 90  QAWDGTTDY 98

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.8 bits (103), Expect = 4e-06
 Identities = 10/42 (23%), Positives = 17/42 (40%)

Query: 8  NEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
              G   V F   E+A+  ++  +G   GGR+I  +     
Sbjct: 54 RHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGT 95

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.7 bits (126), Expect = 2e-09
 Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 7/88 (7%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            + +         +E+++ FS  G V +V+IP          FAFV F   + A+S    
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSLCG- 60

Query: 278 FNGQKFGKRPIAVDWAVPKNIYSSGGAA 305
                     + +  A PK+  +SG ++
Sbjct: 61  -EDLIIKGISVHISNAEPKHNSNSGPSS 87

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 9e-08
 Identities = 14/86 (16%), Positives = 33/86 (38%), Gaps = 12/86 (13%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           + +F+     D+  +E+++ FS +G+V+             +   F+ F   + A +   
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLCG 60

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKK 511
                    + +KG  + +  A  K 
Sbjct: 61  E-------DLIIKGISVHISNAEPKH 79

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 9/57 (15%), Positives = 19/57 (33%), Gaps = 2/57 (3%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLEQRRS 57
          ++        R F +V FA  + A           + G  + + +A  + +     S
Sbjct: 32 VMDVFIPKPFRAFAFVTFADDQIAQSL--CGEDLIIKGISVHISNAEPKHNSNSGPS 86

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.9 bits (126), Expect = 2e-09
 Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 7/95 (7%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           GG  ++   +++++  +P      ++KD     G V    +  +           V++  
Sbjct: 7   GGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MGMVEYLR 59

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSG 302
           K D E A++K +  KF        +       SSG
Sbjct: 60  KEDMEYALRKLDDTKFRSHEGETSYIRVYPERSSG 94

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 52.4 bits (125), Expect = 2e-09
 Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 3/84 (3%)

Query: 215 QKWKLIIRNIPFKAKVNE-IKDMFSPVG-LVWNVYIPHNTDTGLSKGFAFVKFTCKRDAE 272
           +  +++IRN+  +      +++ F   G +          +   +   AF+ F  K  AE
Sbjct: 3   EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 273 SAIQKFNGQKFGKRPIAVDWAVPK 296
            A+ + N    G R I+V  A  K
Sbjct: 63  RAL-QMNRSLLGNREISVSLADKK 85

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.3 bits (96), Expect = 2e-05
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 8/87 (9%)

Query: 426 NTIFICNLPFDLDNEEVKQRF--SAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAA 483
             I I NL  +L +E + +             +P   +         F+ F+  ++A  A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 484 VSASKTTSGLGIFLKGRQLTVLKALDK 510
           +  +         L  R+++V  A  K
Sbjct: 65  LQMN------RSLLGNREISVSLADKK 85

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 37.8 bits (87), Expect = 4e-04
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHR 49
             +K  + +    ++ F   + A RA++M N + +G R+I V  A  +
Sbjct: 38 PAGQKEHSFNNCCAFMVFENKDSAERALQM-NRSLLGNREISVSLADKK 85

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.7 bits (126), Expect = 3e-09
 Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 1/85 (1%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
             +G ++    + ++    +       +M    G V  + +  N       G  +VKF  
Sbjct: 19  SADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRR 77

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDW 292
           + DAE A+   N + F  +PI  + 
Sbjct: 78  EEDAEKAVIDLNNRWFNGQPIHAEL 102

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.5 bits (125), Expect = 4e-09
 Identities = 14/99 (14%), Positives = 28/99 (28%), Gaps = 15/99 (15%)

Query: 208 GGEGSKTQKWKLIIRNIPFK-----AKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAF 262
           G  GS      LI                + + +F             +           
Sbjct: 1   GSSGSSG----LIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVR 50

Query: 263 VKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSS 301
           + F+    A  A  + +  +F  + + + +A   +I SS
Sbjct: 51  INFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIGSS 89

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.6 bits (123), Expect = 5e-09
 Identities = 19/96 (19%), Positives = 34/96 (35%), Gaps = 10/96 (10%)

Query: 209 GEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
           G G      +L +  +     +  +   F   G +  +             FA++++   
Sbjct: 10  GYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESL 63

Query: 269 RDAESAIQKFNGQKFG--KRPIAVDWAVPKNIYSSG 302
             A++A  K  G   G   R + VD+A      SSG
Sbjct: 64  DAAQAACAKMRGFPLGGPDRRLRVDFAKSGP--SSG 97

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (120), Expect = 1e-08
 Identities = 14/84 (16%), Positives = 32/84 (38%), Gaps = 8/84 (9%)

Query: 215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA 274
           +   L +           ++  FSP G + ++ +         +  AFV +     A+ A
Sbjct: 4   KGNTLYVYGEDMTPT--LLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQA 55

Query: 275 IQKFNGQKFGKRPIAVDWAVPKNI 298
           + + NG +     + V+ A  + +
Sbjct: 56  VAELNGTQVESVQLKVNIARKQPM 79

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 13/37 (35%), Positives = 19/37 (51%)

Query: 10 HRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHA 46
           R   +V +  ME A++AV   NGT V   ++ V  A
Sbjct: 38 PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 74

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 50.3 bits (119), Expect = 1e-08
 Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 3/88 (3%)

Query: 210 EGSK-TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK 268
           EGS+ T  + L I N+     V E+K   S +    ++ +     TG ++ F +V F   
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESA 64

Query: 269 RDAESAIQKFNGQKFGKRPIAVDWAVPK 296
            D E A++   G K     I ++    +
Sbjct: 65  EDLEKALE-LTGLKVFGNEIKLEKPKGR 91

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 39.9 bits (92), Expect = 6e-05
 Identities = 17/90 (18%), Positives = 34/90 (37%), Gaps = 7/90 (7%)

Query: 421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAA 480
           E      +FI NL  +    E+K   S          V  + T   +  G++ F++ E  
Sbjct: 9   ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDL 67

Query: 481 TAAVSASKTTSGLGIFLKGRQLTVLKALDK 510
             A+  +      G+ + G ++ + K   +
Sbjct: 68  EKALELT------GLKVFGNEIKLEKPKGR 91

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 2e-08
 Identities = 17/77 (22%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           K+ +  I    + + ++D F   G +  + I  +  +G  +GFAFV F    D+   I  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD-DHDSVDKIVI 62

Query: 278 FNGQKFGKRPIAVDWAV 294
                       V  A+
Sbjct: 63  QKYHTVNGHNCEVRKAL 79

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 8e-08
 Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 6/82 (7%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
            IF+  +  D +   ++  F  +G++     +  + + + +G  F+ F   ++    V  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 63

Query: 487 SKTTSGLGIFLKGRQLTVLKAL 508
                     + G    V KAL
Sbjct: 64  K------YHTVNGHNCEVRKAL 79

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.7 bits (118), Expect = 3e-08
 Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 3/97 (3%)

Query: 208 GGEGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTC 267
           G     T    + +R +P++A  N+I + FSP+  +           G   G A V+F  
Sbjct: 7   GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD--GRVTGEADVEFAT 64

Query: 268 KRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSSGGA 304
             DA +A+ K +      R + +          SG +
Sbjct: 65  HEDAVAAMAK-DKANMQHRYVELFLNSTAGTSGSGPS 100

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 3e-04
 Identities = 20/101 (19%), Positives = 38/101 (37%), Gaps = 13/101 (12%)

Query: 407 SSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRP 466
           SS S   S + T G     + + +  LP+     ++   FS    +   + +      R 
Sbjct: 2   SSGSSGSSFQSTTG-----HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD--GRV 54

Query: 467 KGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
            G   ++F T E A AA++  K        ++ R + +   
Sbjct: 55  TGEADVEFATHEDAVAAMAKDKAN------MQHRYVELFLN 89

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 2e-07
 Identities = 13/70 (18%), Positives = 24/70 (34%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L IR +       ++  +  P G + +     +  T   KG+ FV F     A+ A+   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 279 NGQKFGKRPI 288
                  +  
Sbjct: 61  KASGVQAQMA 70

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 3e-05
 Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSAS 487
           ++I  L     ++++ +    +G++VS   +L + T + KG GF+ F +  AA  AV+A 
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 488 KTTSGLGIFLKGRQL 502
           K        ++ +  
Sbjct: 61  K-----ASGVQAQMA 70

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.2 bits (111), Expect = 3e-07
 Identities = 24/95 (25%), Positives = 42/95 (44%), Gaps = 8/95 (8%)

Query: 208 GGEGSKTQ-KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFT 266
           G  GS  + K  ++ +N+P      EI++ FS  G +  V +P           A V+F 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEFL 54

Query: 267 CKRDAESAIQKFNGQKFGKRPIAVDWAVPKNIYSS 301
              +A  A +     KF   P+ ++WA P  ++ +
Sbjct: 55  EPLEARKAFRHLAYSKFHHVPLYLEWA-PIGVFGA 88

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.1 bits (111), Expect = 3e-07
 Identities = 12/103 (11%), Positives = 28/103 (27%), Gaps = 18/103 (17%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           + +R +       ++ +     G +  V +            A V+F     A+  +   
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVTFA 71

Query: 279 NGQKF--GKRPIAVDWAVPKNIYSSGGAAAGVQNKGDGNSDSG 319
                    +    +++  K I             G+    SG
Sbjct: 72  ADVPVYIAGQQAFFNYSTSKRI----------TRPGNSGPSSG 104

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.2 bits (93), Expect = 8e-05
 Identities = 10/96 (10%), Positives = 35/96 (36%), Gaps = 9/96 (9%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + +  L   +   ++ +    FG +   + +  +          ++F+ +++A   V 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECV- 68

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKS 521
                + + +++ G+Q     +  K++        S
Sbjct: 69  --TFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPS 102

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 3e-07
 Identities = 19/90 (21%), Positives = 41/90 (45%), Gaps = 8/90 (8%)

Query: 421 EDELQN-TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEA 479
           +++++N +++I   P D   +++K+     G+V++       + K  KG+ F+ F ++E+
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR-RTLHKAFKGSIFVVFDSIES 59

Query: 480 ATAAVSASKTTSGLGIFLKGRQLTVLKALD 509
           A   V             K   L +L   D
Sbjct: 60  AKKFVETPGQK------YKETDLLILFKDD 83

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 3e-06
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDA 271
           +  +   + I+  P  A +++IK+     G V N      T     KG  FV F     A
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESA 60

Query: 272 ESAIQKFNGQKFGKRPIAVDWA 293
           +  ++   GQK+ +  + + + 
Sbjct: 61  KKFVET-PGQKYKETDLLILFK 81

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.2 bits (111), Expect = 3e-07
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAE 272
               + + ++ +PF+A+   + D F  + +V +         G + G  FV+F  + D +
Sbjct: 15  HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYK 74

Query: 273 SAIQKFNGQKFGKRPIAVDWAVPKN 297
           +A+ +   Q  G R I V     K 
Sbjct: 75  AALCRHK-QYMGNRFIQVHPITKKG 98

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (95), Expect = 4e-05
 Identities = 18/116 (15%), Positives = 44/116 (37%), Gaps = 6/116 (5%)

Query: 410 SKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGT 469
              +   ++    E    +++  LPF+ +N+ V   F     V   + + +    +  G 
Sbjct: 3   PSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGE 62

Query: 470 GFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNET 525
           GF++F+      AA+   K        +  R + V     K +    ++ + + ++
Sbjct: 63  GFVEFRNEADYKAALCRHKQY------MGNRFIQVHPITKKGMLEKIDMIRKRLQS 112

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 6e-07
 Identities = 19/78 (24%), Positives = 28/78 (35%), Gaps = 1/78 (1%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L I N+P      E+++M  P G            +G S+G  F +       E+ I  
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFG-QVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 78

Query: 278 FNGQKFGKRPIAVDWAVP 295
           FNG+     P       P
Sbjct: 79  FNGKFIKTPPGVSAPTEP 96

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.2 bits (93), Expect = 7e-05
 Identities = 22/103 (21%), Positives = 44/103 (42%), Gaps = 9/103 (8%)

Query: 405 LNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTK 464
           L +S  + +  KQ   +++    ++I NLP  +D +E++     FG+V+S   +    + 
Sbjct: 1   LKASGVQAQMAKQ---QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRIL-RDSSG 56

Query: 465 RPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA 507
             +G GF + ++ E   A +         G F+K         
Sbjct: 57  TSRGVGFARMESTEKCEAVIGHFN-----GKFIKTPPGVSAPT 94

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.8 bits (105), Expect = 1e-06
 Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 215 QKWKLIIRNIPFKAKVNEI---KDMFSPVGLVWNVYIPHNTDTGLS---KGFAFVKFTCK 268
           QK  + +  +  +    E+    + F   G +  V I ++T    S      A+V +   
Sbjct: 7   QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 66

Query: 269 RDAESAIQKFNGQKFGKRPIAV 290
            DA  AIQ  N      R +  
Sbjct: 67  EDALRAIQCVNNVVVDGRTLKA 88

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.9 bits (87), Expect = 4e-04
 Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 5/82 (6%)

Query: 426 NTIFICNLPFDLDNEEVKQRF---SAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATA 482
           N +F+  L   L + EV +R      FG++   V          +G     + T   +  
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 483 AVSASKTTSGLGIFLKGRQLTV 504
           A+ A +  +   + + GR L  
Sbjct: 69  ALRAIQCVN--NVVVDGRTLKA 88

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 19/89 (21%), Positives = 34/89 (38%), Gaps = 10/89 (11%)

Query: 211 GSKTQKWKLIIRNIPFKA-KVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKR 269
           G+      L++ N+  +      +  +F   G V  V I  N         A V+     
Sbjct: 1   GNSV----LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGN 51

Query: 270 DAESAIQKFNGQKFGKRPIAVDWAVPKNI 298
            A+ A+   NG K   +PI +  +  +N+
Sbjct: 52  QAQLAMSHLNGHKLHGKPIRITLSKHQNV 80

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 4e-04
 Identities = 15/105 (14%), Positives = 35/105 (33%), Gaps = 9/105 (8%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
           + + + NL  +    +           V  V +L    +       ++      A  A+S
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN----ALVQMADGNQAQLAMS 58

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEIDKSKNETNDHRN 530
                   G  L G+ + +  +  + +   +E  + +  T D+ N
Sbjct: 59  HLN-----GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGN 98

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.5 bits (104), Expect = 2e-06
 Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 8/83 (9%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L IR +P +    E+  +  P G V N+ +    +       AF++   +  A + +  
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN------QAFLELATEEAAITMVNY 63

Query: 278 F--NGQKFGKRPIAVDWAVPKNI 298
           +         +PI + ++  K +
Sbjct: 64  YSAVTPHLRNQPIYIQYSNHKEL 86

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.5 bits (86), Expect = 4e-04
 Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 15/93 (16%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
             + I  LP ++   EV            F  V + +  + K   FL+  T EAA   V+
Sbjct: 9   RVLHIRKLPGEVTETEVIALGL------PFGKVTNILMLKGKNQAFLELATEEAAITMVN 62

Query: 486 ASKTTSGLGIFLKGRQLTVLKALDKKLAHDKEI 518
                  +   L+ + + +      + ++ KE+
Sbjct: 63  YYS---AVTPHLRNQPIYI------QYSNHKEL 86

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 43.7 bits (102), Expect = 3e-06
 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 6/77 (7%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            L + N+P +     +  +F+       V +  N         AFV+FT +  + +A + 
Sbjct: 10  ILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFTTELQSNAAKEA 64

Query: 278 FNGQKFGK-RPIAVDWA 293
             G K      + + +A
Sbjct: 65  LQGFKITPTHAMKITFA 81

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 3e-06
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 8/79 (10%)

Query: 426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS 485
            T+ + N+P  +  E++K  FS+ G VV       +  K       ++  +VE A  A+ 
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM----ALIQMGSVEEAVQALI 66

Query: 486 ASKTTSGLGIFLKGRQLTV 504
                       +   L V
Sbjct: 67  DLHNHD----LGENHHLRV 81

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 1e-05
 Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 5/76 (6%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           L + NIP      ++K +FS  G V   +     D    +  A ++     +A  A+   
Sbjct: 13  LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDL 68

Query: 279 NGQKFGK-RPIAVDWA 293
           +    G+   + V ++
Sbjct: 69  HNHDLGENHHLRVSFS 84

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.8 bits (97), Expect = 1e-05
 Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 7/75 (9%)

Query: 219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF 278
           ++IR +P      E+ D+ S        Y          KG AFV       AE+AI  F
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSD-------YELKYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 279 NGQKFGKRPIAVDWA 293
           +  +  +R ++V   
Sbjct: 54  HQSRLRERELSVQLQ 68

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.8 bits (95), Expect = 3e-05
 Identities = 14/92 (15%), Positives = 35/92 (38%), Gaps = 13/92 (14%)

Query: 205 RQLGGEGSKTQKWKLIIRNIPF-KAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFV 263
           ++   E  +     + I +    K    ++  +  P G++ N  I +  +       AF+
Sbjct: 1   QKGRVETRRV----VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN------EAFI 50

Query: 264 KFTCKRDAESAIQKF--NGQKFGKRPIAVDWA 293
           +     DA++A+  +         +P+ V  +
Sbjct: 51  EMATTEDAQAAVDYYTTTPALVFGKPVRVHLS 82

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 18/94 (19%), Positives = 35/94 (37%), Gaps = 10/94 (10%)

Query: 419 EGEDELQNTIFICNLPFDLDNE-EVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTV 477
           +G  E +  + I +     +   ++ Q    FG + + + +            F++  T 
Sbjct: 2   KGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN------EAFIEMATT 55

Query: 478 EAATAAVSASKTTSGLGIFLKGRQLTVLKALDKK 511
           E A AAV    TT      + G+ + V  +   K
Sbjct: 56  EDAQAAVDYYTTT---PALVFGKPVRVHLSQKYK 86

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.6 bits (94), Expect = 4e-05
 Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 7/79 (8%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
           ++++  +P      ++KD     G V    +  +           V+F  K D   A++K
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAVRK 54

Query: 278 FNGQKFGKRPIAVDWAVPK 296
            +  KF        +   K
Sbjct: 55  LDNTKFRSHEGETAYIRVK 73

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 7e-05
 Identities = 13/89 (14%), Positives = 33/89 (37%), Gaps = 9/89 (10%)

Query: 214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAES 273
           TQ   +    +      N++  +    GLV  + +P N        ++F ++    +++ 
Sbjct: 18  TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKR 71

Query: 274 AIQKFNGQKFG---KRPIAVDWAVPKNIY 299
           A    NG++      + I +     + + 
Sbjct: 72  AYVTLNGKEVVDDLGQKITLYLNFVEKVQ 100

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.7 bits (89), Expect = 1e-04
 Identities = 13/76 (17%), Positives = 30/76 (39%), Gaps = 3/76 (3%)

Query: 218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQK 277
            ++++N+P     N++   F   G + +V +  +     +  FA ++F     A +    
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALA-AIT 58

Query: 278 FNGQKFGKRPIAVDWA 293
              +  G+  I V   
Sbjct: 59  KTHKVVGQNEIIVSHL 74

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 36.0 bits (82), Expect = 0.001
 Identities = 13/81 (16%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSA 486
           T+ + NLP   +  +V + F   G ++     +    K+      ++F   + A AA++ 
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHV--DVADSLKKNFRFARIEFARYDGALAAITK 59

Query: 487 SKTTSGLGIFLKGRQLTVLKA 507
           +         +   ++ V   
Sbjct: 60  T------HKVVGQNEIIVSHL 74

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 8/53 (15%), Positives = 20/53 (37%)

Query: 1  MVTKKGSNEHRGFGYVQFAVMEDANRAVEMKNGTSVGGRKIGVKHAMHRASLE 53
           + K   +    + ++++     A +A+            IGVK  + +  +E
Sbjct: 29 NILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKNVME 81

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.8 bits (85), Expect = 7e-04
 Identities = 10/68 (14%), Positives = 20/68 (29%), Gaps = 6/68 (8%)

Query: 231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV 290
           + I   F+                  +  +  +++  K  A  A+ K          I V
Sbjct: 18  SYILLQFAQY------GNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGV 71

Query: 291 DWAVPKNI 298
              + KN+
Sbjct: 72  KPCIDKNV 79

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	676
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.96
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.95
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.78
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.77
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.77
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.77
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.77
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.76
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.76
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.76
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.76
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.76
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.76
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.75
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.75
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.75
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.74
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.74
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.74
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.74
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.74
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.73
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.73
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.73
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.73
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.73
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.73
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.72
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.72
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.72
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.72
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.72
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.71
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.71
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.71
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.71
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.71
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.71
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.71
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.7
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.7
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.7
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.7
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.7
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.7
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.7
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.7
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.7
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.7
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.69
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.69
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.69
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.69
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.69
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.69
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.69
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.69
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.69
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.68
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.68
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.68
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.68
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.67
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.67
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.67
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.67
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.67
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.67
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.67
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.66
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.66
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.66
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.65
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.65
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.65
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.64
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.64
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.64
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.64
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.64
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.63
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.63
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.63
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.63
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.63
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.63
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.63
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.63
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.62
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.62
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.62
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.62
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.62
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.61
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.61
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.61
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.61
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.61
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.61
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.61
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.61
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.61
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.61
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.6
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.6
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.6
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.6
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.6
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.6
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.6
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.59
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.59
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.59
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.59
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.59
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.58
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.58
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.58
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.58
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.58
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.58
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.58
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.57
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.57
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.57
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.57
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.56
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.56
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.56
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.56
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.56
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.55
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.55
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.55
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.55
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.54
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.54
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.54
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.53
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.53
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.53
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.53
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.52
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.52
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.52
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.52
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.51
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.5
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.49
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.42
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.41
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.38
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.36
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.35
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.34
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.34
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.32
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.3
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.28
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.26
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.26
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.2
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.2
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.19
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.12
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.3
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.18
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.07
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.61
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.58
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.32
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.85
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	93.83

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=2.2e-28  Score=231.09  Aligned_cols=174  Identities=20%  Similarity=0.340  Sum_probs=152.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      ++|||+|||+++|+++|+++|++||.|.++.++++..++.++|||||+|.+.++|.+|+.. ++..+.++.+.+.+..+.
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCCT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhhc
Confidence            6999999999999999999999999999999999988999999999999999999999994 788888888888876443


Q ss_pred             CCCCcCCcccCccCCCCCCCCCCCCCCCCCCcccccCCCCCCccccCCCCCCCchhHHHHHHHHhhcccccCCCCCCCCC
Q 005812          297 NIYSSGGAAAGVQNKGDGNSDSGSDDDLGDDDAETASDDSNSSEKEDLPSNADFDEEVDIARKVLNKLTSTTGSLPSLSD  376 (676)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  376 (676)
                      ......                                                                          
T Consensus        86 ~~~~~~--------------------------------------------------------------------------   91 (183)
T d1u1qa_          86 EDSQRP--------------------------------------------------------------------------   91 (183)
T ss_dssp             TGGGST--------------------------------------------------------------------------
T ss_pred             cccccc--------------------------------------------------------------------------
Confidence            210000                                                                          


Q ss_pred             ccccccCCCCCCCchhhccccccccccccCCCCCCCCCCCcccCCCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEE
Q 005812          377 DSALVKGNKEQDSDKTVNESAKVSDVSKLNSSKSKPKSLKQTEGEDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFV  456 (676)
Q Consensus       377 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~  456 (676)
                                                                 ......++|||+|||+.+|+++|+++|+.||.|..+.
T Consensus        92 -------------------------------------------~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~  128 (183)
T d1u1qa_          92 -------------------------------------------GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE  128 (183)
T ss_dssp             -------------------------------------------TTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEE
T ss_pred             -------------------------------------------ccccccceeEEccCCCcCCHHHHhhhhccCCceeeee
Confidence                                                       0111246999999999999999999999999999999


Q ss_pred             EeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEccCchhhh
Q 005812          457 PVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKALDKKLAH  514 (676)
Q Consensus       457 i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a~~k~~~~  514 (676)
                      |+.+..++.++|||||+|.+.++|.+|++ ++     +..|+|+.|.|.+|.+|++..
T Consensus       129 i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~-----~~~~~G~~i~V~~A~~k~e~~  180 (183)
T d1u1qa_         129 IMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QK-----YHTVNGHNCEVRKALSKQEMA  180 (183)
T ss_dssp             EEECTTTCCEEEEEEEEESCHHHHHHHHT-SS-----CEEETTEEEEEEECCCHHHHH
T ss_pred             eecccccCccceeEEEEECCHHHHHHHHH-hC-----CCeECCEEEEEEecCCccccc
Confidence            99998889999999999999999999996 67     889999999999999876543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=3.2e-27  Score=223.02  Aligned_cols=166  Identities=19%  Similarity=0.250  Sum_probs=147.3

Q ss_pred             CcEEEEcCCCccccHHHHHHHhhcCCCeEEEEeeCCchhhhhcccccCCCccceEEEEeCCHHHHHHHHHHhCCCeecCe
Q 005812          121 ARTVIIGGLLNADMAEEVHRLAGSIGTVCSVTYPLPKEELEQHGLAQEGCKMDASAVLYTTVKSACASVALLHQKEIKGG  200 (676)
Q Consensus       121 ~~~l~V~nLp~~~~~~~l~~~F~~~G~v~~v~~~~~~~~~~~~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~~~~~~~~  200 (676)
                      .|+|||+|||+.+++++|+++|++||.|.++.++.+..         .|.++|||||+|.+.++|.+|+. +++..+.++
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~---------~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~   75 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN---------TKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGR   75 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT---------TCCEEEEEEEEESSHHHHHHHHH-TCSCEETTE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeeccc---------CCCccCceecccCCHHHHHHHHH-hcCCccccc
Confidence            47999999999999999999999999999999887653         48899999999999999999998 566777888


Q ss_pred             EEEEecCCC------CCCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHH
Q 005812          201 TVWARQLGG------EGSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESA  274 (676)
Q Consensus       201 ~i~v~~~~~------~~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A  274 (676)
                      .+.+.....      .......++|||+|||+.+++++|+++|+.||.|..+.|+.+..+|.++|||||+|.+.++|.+|
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~A  155 (183)
T d1u1qa_          76 VVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI  155 (183)
T ss_dssp             ECEEEECCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHH
T ss_pred             chhhhhhhhcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHH
Confidence            777654322      22345568999999999999999999999999999999999988999999999999999999999


Q ss_pred             HHHhCCceeCCeeEEEEEecCCC
Q 005812          275 IQKFNGQKFGKRPIAVDWAVPKN  297 (676)
Q Consensus       275 ~~~l~~~~~~g~~i~v~~a~~~~  297 (676)
                      ++ +++..+.|+.|+|.||.++.
T Consensus       156 l~-~~~~~~~G~~i~V~~A~~k~  177 (183)
T d1u1qa_         156 VI-QKYHTVNGHNCEVRKALSKQ  177 (183)
T ss_dssp             HT-SSCEEETTEEEEEEECCCHH
T ss_pred             HH-hCCCeECCEEEEEEecCCcc
Confidence            98 69999999999999997754

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.78  E-value=4.9e-19  Score=144.00  Aligned_cols=82  Identities=22%  Similarity=0.338  Sum_probs=78.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      .+++|||+|||..+++++|+++|+.||.|.+|++++++.+|.++|||||+|.+.++|.+|+..||     |..|+|+.|.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~ln-----g~~l~g~~l~   80 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN-----GAEIMGQTIQ   80 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHT-----TCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcC-----CCEECCEEEE
Confidence            46899999999999999999999999999999999999999999999999999999999999999     9999999999


Q ss_pred             EEEccCc
Q 005812          504 VLKALDK  510 (676)
Q Consensus       504 v~~a~~k  510 (676)
                      |.||.+|
T Consensus        81 V~~a~~k   87 (88)
T d1rk8a_          81 VDWCFVK   87 (88)
T ss_dssp             EEESEEC
T ss_pred             EEEecCC
Confidence            9999875

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.77  E-value=8.7e-19  Score=142.48  Aligned_cols=85  Identities=29%  Similarity=0.546  Sum_probs=79.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      ...+.++|||+|||..+++++|+++|+.||.|.+|++++++.+|.++|||||+|.+.++|++|+..|||..+.|+.|+|+
T Consensus         3 ~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~   82 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD   82 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCC
Q 005812          292 WAVPK  296 (676)
Q Consensus       292 ~a~~~  296 (676)
                      |+.++
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            99765

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.77  E-value=6.1e-19  Score=141.69  Aligned_cols=80  Identities=30%  Similarity=0.514  Sum_probs=77.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      +++|||+|||.++++++|+++|++||.|.++.+++++.+|.++|||||+|.+.++|++|++.|||..+.|+.|+|.|++|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            56899999999999999999999999999999999988999999999999999999999999999999999999999976

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=7.4e-19  Score=147.12  Aligned_cols=85  Identities=26%  Similarity=0.386  Sum_probs=80.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      +++++|||+|||+++++++|+++|+.||.|.++.++.+..+|.++|||||+|.+.++|.+|+..||     |..|+|+.|
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~ln-----g~~~~g~~i   90 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMN-----GFQIGMKRL   90 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHT-----TCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhC-----CCEECCEEE
Confidence            456899999999999999999999999999999999999999999999999999999999999999     999999999


Q ss_pred             EEEEccCchh
Q 005812          503 TVLKALDKKL  512 (676)
Q Consensus       503 ~v~~a~~k~~  512 (676)
                      .|.||.++..
T Consensus        91 ~V~~a~~k~~  100 (102)
T d2cpza1          91 KVQLKRSKND  100 (102)
T ss_dssp             EEECCCCSCC
T ss_pred             EEEEeCCCCC
Confidence            9999988753

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.77  E-value=5.8e-19  Score=141.82  Aligned_cols=80  Identities=21%  Similarity=0.323  Sum_probs=77.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      +++|||+|||+.+++++|+++|++||.|.++++++++.+|.++|||||+|.++++|++|++.||     |..|+|++|+|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~ln-----g~~~~g~~l~v   76 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLN-----GITVRNKRLKV   76 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHT-----TCEETTEECEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhC-----CCEECCEEEEE
Confidence            3689999999999999999999999999999999998899999999999999999999999999     99999999999


Q ss_pred             EEccC
Q 005812          505 LKALD  509 (676)
Q Consensus       505 ~~a~~  509 (676)
                      .||+|
T Consensus        77 ~~a~p   81 (82)
T d1b7fa1          77 SYARP   81 (82)
T ss_dssp             EECCC
T ss_pred             EEcCC
Confidence            99875

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

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

Probab=99.76  E-value=1.7e-18  Score=141.50  Aligned_cols=85  Identities=27%  Similarity=0.590  Sum_probs=80.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||..+++++|+++|+.||.|.+|.|+.++.+|.++|||||+|.+.++|.+|++.|+|..|+|+.|.|.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            44567999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 005812          293 AVPKN  297 (676)
Q Consensus       293 a~~~~  297 (676)
                      +.|+.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            98763

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=8.4e-19  Score=142.98  Aligned_cols=83  Identities=29%  Similarity=0.442  Sum_probs=79.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++|||+|||+++++++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|+.|++.|||..|.|+.|.|.|+.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 005812          295 PKN  297 (676)
Q Consensus       295 ~~~  297 (676)
                      |+.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.7e-18  Score=139.00  Aligned_cols=80  Identities=30%  Similarity=0.544  Sum_probs=77.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      .++|||+|||+++++++|+++|++||.|.+|+++++..+|.++|||||+|.+.++|+.|++.|||..|.|+.|+|.|++|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            46799999999999999999999999999999999988999999999999999999999999999999999999999976

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

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

Probab=99.76  E-value=1.1e-18  Score=142.65  Aligned_cols=83  Identities=24%  Similarity=0.298  Sum_probs=79.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      +.++|||+|||..+++++|+++|++||.|.+|.++.+..++.++|||||+|.+.++|.+|++.||     |..|+|+.|.
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~-----g~~~~g~~i~   81 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVS-----GFGYDHLILN   81 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTT-----TCEETTEECE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhC-----CCEECCEEEE
Confidence            45799999999999999999999999999999999998899999999999999999999999999     9999999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.||+++.
T Consensus        82 v~~akp~~   89 (90)
T d2cq0a1          82 VEWAKPST   89 (90)
T ss_dssp             EEESSCCC
T ss_pred             EEeeeCCC
Confidence            99998763

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2.1e-18  Score=141.67  Aligned_cols=82  Identities=21%  Similarity=0.273  Sum_probs=78.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      .+++|||+|||+.+|+++|+++|++||.|.+|.++.++.++.++|||||+|.+.++|..|++.||     |..|+|++|.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~-----g~~~~gr~i~   80 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYIN-----GTRLDDRIIR   80 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTT-----TSEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhC-----CCEECCEEEE
Confidence            46899999999999999999999999999999999999999999999999999999999999999     9999999999


Q ss_pred             EEEccCc
Q 005812          504 VLKALDK  510 (676)
Q Consensus       504 v~~a~~k  510 (676)
                      |.|+...
T Consensus        81 V~~a~~~   87 (93)
T d1h2vz_          81 TDWDAGF   87 (93)
T ss_dssp             EEEESCC
T ss_pred             EEEcCCC
Confidence            9998754

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=8.2e-19  Score=143.06  Aligned_cols=81  Identities=23%  Similarity=0.386  Sum_probs=78.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+++++++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|.+|+..||     +..|+|++|.|
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~-----~~~i~g~~l~v   79 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN-----ESELFGRTIRV   79 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHT-----TEEETTEEEEE
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcC-----CCEECCEEEEE
Confidence            4799999999999999999999999999999999999999999999999999999999999999     99999999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      .+|.++
T Consensus        80 ~~a~p~   85 (89)
T d2cqba1          80 NLAKPM   85 (89)
T ss_dssp             EECCCC
T ss_pred             EEeCCC
Confidence            999875

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

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=99.75  E-value=1.8e-18  Score=142.09  Aligned_cols=86  Identities=27%  Similarity=0.400  Sum_probs=81.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||..+++++|+++|++||.|.+|.|++++.+|.++|||||+|.+.++|..|++.|||..|.|+.|+|.
T Consensus         5 ~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   84 (93)
T d1x5ua1           5 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   84 (93)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      ||.++.
T Consensus        85 ~A~~~~   90 (93)
T d1x5ua1          85 KASAHN   90 (93)
T ss_dssp             ETTTTS
T ss_pred             EcCCCC
Confidence            998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.8e-18  Score=137.92  Aligned_cols=77  Identities=18%  Similarity=0.360  Sum_probs=75.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEE
Q 005812          427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLK  506 (676)
Q Consensus       427 ~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~  506 (676)
                      +|||+|||+.+|+++|+++|++||.|.+|+|++++.+|.++|||||+|.++++|..|++.|+     |..++||+|+|.|
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~-----g~~~~gr~i~v~~   76 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMN-----FDVIKGKPVRIMW   76 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTST-----TCEETTEECEEEE
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcC-----CCEECCEEEEEEE
Confidence            69999999999999999999999999999999999999999999999999999999999999     9999999999999


Q ss_pred             cc
Q 005812          507 AL  508 (676)
Q Consensus       507 a~  508 (676)
                      |.
T Consensus        77 a~   78 (80)
T d1cvja1          77 SQ   78 (80)
T ss_dssp             CC
T ss_pred             eC
Confidence            85

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

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=99.75  E-value=1.2e-18  Score=143.17  Aligned_cols=83  Identities=25%  Similarity=0.291  Sum_probs=79.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      ..++|||+|||+.+|+++|+++|++||.|.+|+|+.++.++.++|||||+|.+.++|.+|++.||     |..|+|+.|.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~-----g~~~~g~~l~   82 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMD-----MIKLYGKPIR   82 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSS-----SCBCSSCBCE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcC-----CCEECCEEEE
Confidence            35799999999999999999999999999999999999999999999999999999999999999     9999999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.||.++.
T Consensus        83 V~~A~~~~   90 (93)
T d1x5ua1          83 VNKASAHN   90 (93)
T ss_dssp             EEETTTTS
T ss_pred             EEEcCCCC
Confidence            99998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.5e-18  Score=138.11  Aligned_cols=79  Identities=24%  Similarity=0.417  Sum_probs=76.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      ++|||+|||+.+++++|+++|++||.|..|+++.+..++.++|||||+|.++++|.+|++.||     |..|+|++|.|.
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~-----g~~~~g~~l~v~   77 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN-----GLRLQTKTIKVS   77 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-----TCEETTEECEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhC-----CCEECCEEEEEE
Confidence            579999999999999999999999999999999998899999999999999999999999999     999999999999


Q ss_pred             EccC
Q 005812          506 KALD  509 (676)
Q Consensus       506 ~a~~  509 (676)
                      ||+|
T Consensus        78 ~AkP   81 (82)
T d1fxla1          78 YARP   81 (82)
T ss_dssp             ECCC
T ss_pred             EeeC
Confidence            9875

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=6.3e-18  Score=140.79  Aligned_cols=86  Identities=27%  Similarity=0.398  Sum_probs=80.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|+.++.+++++|||||+|.+.++|.+|++.||+..|.|+.|+|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 005812          293 AVPKNI  298 (676)
Q Consensus       293 a~~~~~  298 (676)
                      +.++..
T Consensus        85 a~~~~~   90 (99)
T d1whwa_          85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             CCCCCc
Confidence            987653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=5.8e-18  Score=138.99  Aligned_cols=84  Identities=25%  Similarity=0.458  Sum_probs=79.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ...+++|||+|||+++++++|+++|+.||.|.+|.++.++.++.++|||||+|.+.++|..|++.|||..+.|+.|+|+|
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCC
Q 005812          293 AVPK  296 (676)
Q Consensus       293 a~~~  296 (676)
                      +...
T Consensus        84 a~~~   87 (93)
T d1h2vz_          84 DAGF   87 (93)
T ss_dssp             ESCC
T ss_pred             cCCC
Confidence            8543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2.9e-18  Score=136.70  Aligned_cols=77  Identities=23%  Similarity=0.417  Sum_probs=75.1

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       218 ~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      +|||+|||+.+++++|+++|++||.|.+|+|++++.+|+++|||||+|.++++|..|++.|+|..+.|++|+|.|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999984

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=3.6e-18  Score=138.96  Aligned_cols=81  Identities=25%  Similarity=0.407  Sum_probs=75.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      .+++|||+|||+++|+++|+++|++||.|..|+|++|+.+|.++|||||+|.++++|.+|++.       ...|+||.|.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~-------~~~l~Gr~i~   79 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-------RHMIDGRWCD   79 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS-------CEEETTEEEE
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc-------CCccCCEEeE
Confidence            457899999999999999999999999999999999999999999999999999999999984       4589999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.+|.+++
T Consensus        80 v~~a~~k~   87 (90)
T d2cqga1          80 CKLPNSKQ   87 (90)
T ss_dssp             EECCCTTC
T ss_pred             EEeCCCCC
Confidence            99998864

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.1e-18  Score=136.97  Aligned_cols=77  Identities=23%  Similarity=0.460  Sum_probs=73.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .++++|||+|||+.+|+++|+++|++||.|.+|.|++++.++.++|||||+|.+.++|.+|+..||     +..|+||+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~-----g~~~~gr~i   81 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN-----GMELDGRRI   81 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHT-----TEEETTEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcC-----CCEECCEEe
Confidence            346899999999999999999999999999999999999899999999999999999999999999     999999999


Q ss_pred             EE
Q 005812          503 TV  504 (676)
Q Consensus       503 ~v  504 (676)
                      +|
T Consensus        82 ~V   83 (83)
T d2cqca1          82 RV   83 (83)
T ss_dssp             EE
T ss_pred             EC
Confidence            87

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.74  E-value=4.1e-18  Score=137.61  Aligned_cols=79  Identities=25%  Similarity=0.527  Sum_probs=75.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC--cE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG--RQ  501 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g--r~  501 (676)
                      .+++|||+|||+.+++++|+++|++||.|..+++++++.++.++|||||+|.+.++|.+|++.||     +..+.|  ++
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~-----g~~~~g~~~~   79 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN-----NVIPEGGSQP   79 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-----TCCCTTCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHC-----CCEeCCCCeE
Confidence            45789999999999999999999999999999999999999999999999999999999999999     888876  89


Q ss_pred             EEEEEc
Q 005812          502 LTVLKA  507 (676)
Q Consensus       502 l~v~~a  507 (676)
                      |.|.||
T Consensus        80 l~V~~A   85 (85)
T d1b7fa2          80 LSVRLA   85 (85)
T ss_dssp             CEEEEC
T ss_pred             EEEEEC
Confidence            999986

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=3.8e-18  Score=142.12  Aligned_cols=82  Identities=32%  Similarity=0.526  Sum_probs=78.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|++||.|..|+|+.++.++.++|||||+|.+.++|.+|++.||     +..|+||+|+|
T Consensus         8 ~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~-----g~~~~gr~i~V   82 (99)
T d1whwa_           8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVD-----GQVFQGRMLHV   82 (99)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTT-----TEESSSCEEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcC-----CCEECCEEEEE
Confidence            4689999999999999999999999999999999999999999999999999999999999999     99999999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .+|.++.
T Consensus        83 ~~a~~~~   89 (99)
T d1whwa_          83 LPSTIKK   89 (99)
T ss_dssp             EECCCCS
T ss_pred             EECCCCC
Confidence            9998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=6e-18  Score=141.49  Aligned_cols=84  Identities=30%  Similarity=0.434  Sum_probs=80.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ++.++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|..|++.|||..|.|+.|+|+|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 005812          294 VPKN  297 (676)
Q Consensus       294 ~~~~  297 (676)
                      .++.
T Consensus        96 ~~k~   99 (102)
T d2cpza1          96 RSKN   99 (102)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            8765

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=8e-18  Score=135.21  Aligned_cols=79  Identities=28%  Similarity=0.514  Sum_probs=74.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|++||.|..++|++|..+|.++|||||+|.++++|.+|++ ++     +..|.||.|.|
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~-----~~~i~Gr~i~V   79 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-AR-----PHKVDGRVVEP   79 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TC-----SCEETTEECEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hC-----CCEECCEEEEE
Confidence            3689999999999999999999999999999999999999999999999999999999996 57     88999999999


Q ss_pred             EEccC
Q 005812          505 LKALD  509 (676)
Q Consensus       505 ~~a~~  509 (676)
                      ..|.+
T Consensus        80 ~~A~s   84 (84)
T d1l3ka1          80 KRAVS   84 (84)
T ss_dssp             EECCC
T ss_pred             EeeeC
Confidence            99864

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=2.9e-18  Score=138.26  Aligned_cols=80  Identities=26%  Similarity=0.447  Sum_probs=77.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      .+|||+|||+.+|+++|+++|++||.|..|+|++|+.+|.++|||||+|.++++|..|+..||     +..|+|++|.|.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~-----~~~l~g~~l~V~   76 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN-----GMQLGDKKLLVQ   76 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSS-----SCCCSSSCCEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhC-----CCEECCEEEEEE
Confidence            479999999999999999999999999999999999999999999999999999999999999     999999999999


Q ss_pred             EccCc
Q 005812          506 KALDK  510 (676)
Q Consensus       506 ~a~~k  510 (676)
                      +|.+.
T Consensus        77 ~A~~~   81 (85)
T d2u2fa_          77 RASVG   81 (85)
T ss_dssp             ECCCC
T ss_pred             ECCCC
Confidence            99764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.73  E-value=4.2e-18  Score=136.30  Aligned_cols=79  Identities=13%  Similarity=0.209  Sum_probs=69.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      ++|||+|||+.+|+++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|.+|++.||     |..|+|++|.|.
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~-----g~~~~g~~i~V~   76 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLN-----GLKIEGYTLVTK   76 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHT-----TCEETTEECEEE
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhC-----CCEECCEEEEEE
Confidence            699999999999999999999999999988888888889999999999999999999999999     999999999999


Q ss_pred             EccC
Q 005812          506 KALD  509 (676)
Q Consensus       506 ~a~~  509 (676)
                      ++.|
T Consensus        77 ~a~P   80 (81)
T d2ghpa1          77 VSNP   80 (81)
T ss_dssp             ECCC
T ss_pred             EccC
Confidence            9875

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=3.5e-18  Score=137.77  Aligned_cols=81  Identities=26%  Similarity=0.460  Sum_probs=77.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      .+|||+|||+.+++++|+++|+.||.|.+|+|++++.+|.++|||||+|.++++|..|++.|||..|.|+.|.|.|+.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999764


Q ss_pred             C
Q 005812          297 N  297 (676)
Q Consensus       297 ~  297 (676)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.73  E-value=1.5e-17  Score=147.96  Aligned_cols=85  Identities=22%  Similarity=0.436  Sum_probs=79.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ....++|||+|||+++++++|+++|++||.|.+|+|++++.++.++|||||+|.+.++|.+|++.||     |..|+||.
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~ln-----g~~~~gr~  113 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLN-----GFNILNKR  113 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTT-----TEECSSCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhC-----CCEECCEE
Confidence            3345789999999999999999999999999999999999999999999999999999999999999     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.+|.++.
T Consensus       114 l~V~~a~~~~  123 (139)
T d1u6fa1         114 LKVALAASGH  123 (139)
T ss_dssp             EEEEESSCCC
T ss_pred             EEEEEcCCCC
Confidence            9999987653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=6.8e-18  Score=136.12  Aligned_cols=78  Identities=27%  Similarity=0.488  Sum_probs=74.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC--cEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG--RQL  502 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g--r~l  502 (676)
                      +++|||+|||+.+|+++|+++|++||.|.+++++.++.+|.++|||||+|.++++|.+|++.||     |..+.|  ++|
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~ln-----g~~~~G~~~~i   80 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN-----GQKPSGATEPI   80 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-----TCCCTTCSSCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhC-----CCEeCCCCEEE
Confidence            5789999999999999999999999999999999998899999999999999999999999999     999987  569


Q ss_pred             EEEEc
Q 005812          503 TVLKA  507 (676)
Q Consensus       503 ~v~~a  507 (676)
                      .|.||
T Consensus        81 ~V~~A   85 (85)
T d1fxla2          81 TVKFA   85 (85)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99886

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.72  E-value=1.2e-17  Score=134.83  Aligned_cols=80  Identities=24%  Similarity=0.405  Sum_probs=75.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC--eeEEEE
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK--RPIAVD  291 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g--~~i~v~  291 (676)
                      ...++|||+|||+++++++|+++|++||.|.++++++++.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|.|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            456789999999999999999999999999999999999999999999999999999999999999999976  889999


Q ss_pred             Ee
Q 005812          292 WA  293 (676)
Q Consensus       292 ~a  293 (676)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=5.7e-18  Score=139.34  Aligned_cols=83  Identities=29%  Similarity=0.423  Sum_probs=76.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHc-CCCCCCCeeecCcE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQ-VTKRPKGTGFLKFKTVEAATAAVSAS-KTTSGLGIFLKGRQ  501 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~-~~~~~~g~afV~F~t~~~A~~Al~~l-~~~~~~g~~l~gr~  501 (676)
                      .+++|||+|||+.+++++|+++|++||.|.+|+|+++. .+|.++|||||+|.+.++|.+|+..| |     +..|+|++
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~-----~~~~~Gr~   81 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCH-----STHLYGRR   81 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHT-----CCBSSSCB
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccC-----CcEECCEE
Confidence            45789999999999999999999999999999998874 47899999999999999999999998 8     89999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.||.++.
T Consensus        82 l~V~~A~~~~   91 (94)
T d2cpha1          82 LVLEWADSEV   91 (94)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEcCCCC
Confidence            9999998753

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=8.5e-18  Score=133.15  Aligned_cols=77  Identities=21%  Similarity=0.413  Sum_probs=73.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEE
Q 005812          427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLK  506 (676)
Q Consensus       427 ~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~  506 (676)
                      +|||+|||+.+++++|+++|++||.|.+++++.++ ++.++|||||+|.++++|.+|++.||     |..++|++|.|.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~-----g~~l~g~~l~V~~   75 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYN-----GVPLDGRPMNIQL   75 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHT-----TCEETTEECEEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhC-----CCEECCEEEEEEE
Confidence            69999999999999999999999999999998885 78999999999999999999999999     9999999999999


Q ss_pred             ccC
Q 005812          507 ALD  509 (676)
Q Consensus       507 a~~  509 (676)
                      |.+
T Consensus        76 a~S   78 (78)
T d1no8a_          76 VTS   78 (78)
T ss_dssp             ECC
T ss_pred             eeC
Confidence            853

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.72  E-value=5.2e-18  Score=135.70  Aligned_cols=80  Identities=23%  Similarity=0.329  Sum_probs=70.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      .++|||+|||+++++++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|++|++.|||..+.|+.|.|.++.|
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            36999999999999999999999999999888888888899999999999999999999999999999999999999987

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.2e-17  Score=134.18  Aligned_cols=79  Identities=27%  Similarity=0.395  Sum_probs=74.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      .+.+.++|||+|||+.+++++|+++|++||.|.+|.|+.++.++.++|||||+|.+.++|..|++.|||..|.|+.|+|
T Consensus         5 ~p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           5 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            3445789999999999999999999999999999999999989999999999999999999999999999999999987

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=1.1e-17  Score=137.69  Aligned_cols=85  Identities=34%  Similarity=0.654  Sum_probs=78.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCC-CCCceeEEEEEecCHHHHHHHHHHh-CCceeCCeeEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTD-TGLSKGFAFVKFTCKRDAESAIQKF-NGQKFGKRPIAV  290 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~-~~~~~g~afV~f~~~~~A~~A~~~l-~~~~~~g~~i~v  290 (676)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|+++.. +|.++|||||+|.+.++|.+|++.| ||..|.|+.|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            34567899999999999999999999999999999998754 7899999999999999999999998 899999999999


Q ss_pred             EEecCCC
Q 005812          291 DWAVPKN  297 (676)
Q Consensus       291 ~~a~~~~  297 (676)
                      +|+.+..
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9997653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.2e-17  Score=134.59  Aligned_cols=79  Identities=32%  Similarity=0.531  Sum_probs=74.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC--eeEEEEE
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK--RPIAVDW  292 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g--~~i~v~~  292 (676)
                      .+++|||+|||+.+++++|+++|++||.|.+++|++++.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|.|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            45789999999999999999999999999999999999899999999999999999999999999999987  5699988


Q ss_pred             e
Q 005812          293 A  293 (676)
Q Consensus       293 a  293 (676)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=7.2e-18  Score=140.78  Aligned_cols=81  Identities=22%  Similarity=0.491  Sum_probs=76.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+++++++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|.+|++ ++     +..|+|+.|.|
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~-----~~~l~G~~i~V   93 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-AR-----PHSIDGRVVEP   93 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SC-----SEEETTEEEEE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hC-----CCeECCEEEEE
Confidence            4789999999999999999999999999999999999899999999999999999999995 78     89999999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .+|.+++
T Consensus        94 ~~a~~ke  100 (103)
T d1x4ba1          94 KRAVARE  100 (103)
T ss_dssp             ECCSSCC
T ss_pred             EECcccC
Confidence            9999875

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=9.7e-18  Score=141.05  Aligned_cols=83  Identities=35%  Similarity=0.566  Sum_probs=78.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      ++|||+|||+.+++++|+++|++||.|.+|+++.++.+|.++|||||+|.+.++|.+|++.||     +..|+|++|.|.
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~-----~~~~~g~~i~V~   83 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLN-----GREFSGRALRVD   83 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSS-----SBSCSSSCBEEE
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcC-----CCEECCEEEEEE
Confidence            689999999999999999999999999999999999899999999999999999999999999     999999999999


Q ss_pred             EccCchhh
Q 005812          506 KALDKKLA  513 (676)
Q Consensus       506 ~a~~k~~~  513 (676)
                      +|.++...
T Consensus        84 ~a~~~~~~   91 (104)
T d1p1ta_          84 NAASEKNK   91 (104)
T ss_dssp             ETTCTTHH
T ss_pred             ECCCCCCc
Confidence            99876533

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=2.8e-18  Score=135.22  Aligned_cols=76  Identities=24%  Similarity=0.412  Sum_probs=72.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      |+|||+|||+++|+++|+++|++||.|.+++|++|+.+|.++|||||+|.+.++|.+|++ ++     +..|+||.|.|.
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~-----~~~i~Gr~i~V~   74 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QS-----RHELDSKTIDPK   74 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TT-----TCCCSSCCCEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cC-----CCEECCeEEEEE
Confidence            579999999999999999999999999999999999999999999999999999999996 68     899999999998


Q ss_pred             Ec
Q 005812          506 KA  507 (676)
Q Consensus       506 ~a  507 (676)
                      +|
T Consensus        75 ~A   76 (77)
T d1uawa_          75 VA   76 (77)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

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=99.71  E-value=7.2e-18  Score=135.59  Aligned_cols=79  Identities=34%  Similarity=0.504  Sum_probs=74.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhCCceeEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEE
Q 005812          428 IFICNLPFDLDNEEVKQRFSAFGEVVSF-VPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLK  506 (676)
Q Consensus       428 l~V~nLp~~~teedl~~~F~~~G~v~~v-~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~  506 (676)
                      |||+|||+++++++|+++|++||.|..+ +++++..+|+++|||||+|.++++|.+|++.|+     |..|+|++|.|.+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~-----g~~~~gr~l~v~~   75 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN-----GQYLCNRPITVSY   75 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTT-----TCEETTEECEEEE
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCC-----CcEECCEEEEEEE
Confidence            7999999999999999999999998664 788888899999999999999999999999999     9999999999999


Q ss_pred             ccCch
Q 005812          507 ALDKK  511 (676)
Q Consensus       507 a~~k~  511 (676)
                      |.+++
T Consensus        76 a~~k~   80 (83)
T d1x5ta1          76 AFKKD   80 (83)
T ss_dssp             SCCCC
T ss_pred             ecCCC
Confidence            98764

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=2.2e-17  Score=134.67  Aligned_cols=81  Identities=23%  Similarity=0.279  Sum_probs=74.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      +.++|||+|||..+++++|+++|+.||.|..|+++.+..+  .+|||||+|.+.++|.+|+..|+     |..|.|+.|+
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~-----~~~~~g~~i~   79 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMN-----GRKILGKEVK   79 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHT-----TEEETTEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcC-----CCEECCEEEE
Confidence            3579999999999999999999999999999999988654  38999999999999999999999     9999999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.||.++.
T Consensus        80 v~~a~~~~   87 (90)
T d2cqia1          80 VNWATTPS   87 (90)
T ss_dssp             EEECCCTT
T ss_pred             EEEcCCCC
Confidence            99998653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=2.8e-17  Score=133.54  Aligned_cols=83  Identities=27%  Similarity=0.404  Sum_probs=76.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||+++|+++|+++|+.||.|.+|.|+.++.+|.++|||||+|.+.++|.+||+.  +..|+|+.|.|.+
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~   82 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEEC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEe
Confidence            34567899999999999999999999999999999999999999999999999999999999984  5589999999999


Q ss_pred             ecCCC
Q 005812          293 AVPKN  297 (676)
Q Consensus       293 a~~~~  297 (676)
                      +.++.
T Consensus        83 a~~k~   87 (90)
T d2cqga1          83 PNSKQ   87 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            98764

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=1.9e-17  Score=131.05  Aligned_cols=76  Identities=28%  Similarity=0.489  Sum_probs=73.2

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       218 ~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      +|||+|||+.+++++|+++|++||.|.++.|+.++ +|+++|||||+|.+.++|.+|++.|||..+.|+.|+|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999886 88899999999999999999999999999999999999985

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=8.9e-18  Score=137.30  Aligned_cols=82  Identities=30%  Similarity=0.558  Sum_probs=78.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      ..+|||+|||+.+++++|+++|++||.|..+.++.+..++.++|||||+|.++++|.+|+..|+     |..|+|++|.|
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~-----~~~~~g~~l~V   79 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMN-----GKSVDGRQIRV   79 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHT-----TCCTTSCCCEE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcC-----CCEECCEEEEE
Confidence            4689999999999999999999999999999999988899999999999999999999999999     99999999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .+|.++.
T Consensus        80 ~~a~~~~   86 (90)
T d1x5sa1          80 DQAGKSS   86 (90)
T ss_dssp             EEEECCC
T ss_pred             EEcCCCC
Confidence            9998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1.4e-17  Score=136.18  Aligned_cols=83  Identities=29%  Similarity=0.474  Sum_probs=79.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++|||+|||+++++++|+++|++||.|..+.++.+..+|.++|||||+|.++++|+.|++.|+|..|+|+.|.|.|+.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            55789999999999999999999999999999999988899999999999999999999999999999999999999997


Q ss_pred             CCC
Q 005812          295 PKN  297 (676)
Q Consensus       295 ~~~  297 (676)
                      ++.
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=1.7e-17  Score=134.00  Aligned_cols=78  Identities=28%  Similarity=0.385  Sum_probs=72.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTK---RPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       428 l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~---~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      |||+|||+++|+++|+++|++||.|.+++|++++.++   .++|||||+|.++++|.+|++.||     |..|+|++|.|
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~-----~~~~~g~~i~V   75 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQ-----GHTVDGHKLEV   75 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHST-----TCEETTEECEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhC-----CCEECCEEEEE
Confidence            7999999999999999999999999999999887654   468999999999999999999999     99999999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      .+|.++
T Consensus        76 ~~a~~~   81 (85)
T d2cpfa1          76 RISERA   81 (85)
T ss_dssp             ECSSCS
T ss_pred             EECCCC
Confidence            998654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=9.7e-18  Score=139.55  Aligned_cols=80  Identities=21%  Similarity=0.368  Sum_probs=75.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|+.||.|.+|+|+++..+|.++|||||+|.+.++|.+|+ .||     |..|+|+.|.|
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~-----g~~~~G~~l~V   91 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLT-----GQRLLGVPIIV   91 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHT-----TEEETTEEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHC-----CCEECCEEEEE
Confidence            378999999999999999999999999999999999999999999999999999999999 499     99999999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      .++.++
T Consensus        92 ~~a~~~   97 (101)
T d2cq4a1          92 QASQAE   97 (101)
T ss_dssp             EEHHHH
T ss_pred             EECCCC
Confidence            998654

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

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=99.70  E-value=1.2e-17  Score=134.17  Aligned_cols=79  Identities=34%  Similarity=0.580  Sum_probs=74.5

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCceEEE-EEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCCC
Q 005812          219 LIIRNIPFKAKVNEIKDMFSPVGLVWNV-YIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPKN  297 (676)
Q Consensus       219 v~V~nLp~~~~e~~l~~~F~~~G~i~~v-~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~  297 (676)
                      |||+|||+++++++|+++|++||.|.++ .+++++.+|+++|||||+|.+.++|++|++.|+|..+.|++|+|.|+.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998764 788888899999999999999999999999999999999999999998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=2.4e-17  Score=137.18  Aligned_cols=91  Identities=35%  Similarity=0.487  Sum_probs=81.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCC-CCCeeecCc
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTS-GLGIFLKGR  500 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~-~~g~~l~gr  500 (676)
                      ...+++|||+|||+.+|+++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+|++.|+... .+|..|.||
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3446899999999999999999999999999999999998899999999999999999999999987322 337899999


Q ss_pred             EEEEEEccCchh
Q 005812          501 QLTVLKALDKKL  512 (676)
Q Consensus       501 ~l~v~~a~~k~~  512 (676)
                      .|.|.+|.+|++
T Consensus        85 ~l~v~~a~~k~~   96 (98)
T d1x4ha1          85 QLKVDLAVTRDE   96 (98)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEECCCCCc
Confidence            999999988754

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=3.3e-17  Score=131.56  Aligned_cols=79  Identities=23%  Similarity=0.398  Sum_probs=75.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++|||+|||+++++++|+++|+.||.|.++.|+.++.+|.++|||||+|.+.++|++|++ +++..|.|+.|.|..|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            44789999999999999999999999999999999999999999999999999999999998 59999999999998874

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=4e-17  Score=133.95  Aligned_cols=81  Identities=23%  Similarity=0.532  Sum_probs=75.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      ..++|||+|||+.+++++|+++|++||.|.+|+++.+.  +.++|||||+|.++++|.+|+..||     +..|+|+.|.
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~-----~~~~~g~~l~   82 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLH-----GTVVEGRKIE   82 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHT-----TCEETTEECE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcC-----CCEECCEEEE
Confidence            35789999999999999999999999999999998875  3469999999999999999999999     9999999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.+|.+|.
T Consensus        83 V~~A~~r~   90 (93)
T d2cq3a1          83 VNNATARV   90 (93)
T ss_dssp             EEECCSSC
T ss_pred             EEecCcCC
Confidence            99998864

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=3e-17  Score=137.48  Aligned_cols=80  Identities=24%  Similarity=0.436  Sum_probs=75.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|++||.|.+|+|+.++.+|.++|||||+|.+.++|.+|++.+|     + .|+||+|.|
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~-----~-~l~Gr~l~V   83 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-----P-IIDGRKANV   83 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSS-----C-EETTEECEE
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCC-----C-cCCCEEEEE
Confidence            4689999999999999999999999999999999999999999999999999999999999888     6 699999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      .+|..+
T Consensus        84 ~~a~~~   89 (103)
T d2cqda1          84 NLAYLG   89 (103)
T ss_dssp             EESTTT
T ss_pred             EEcCCC
Confidence            998764

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=6.2e-18  Score=133.22  Aligned_cols=76  Identities=18%  Similarity=0.361  Sum_probs=73.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      |+|||+|||+++++++|+++|++||.|.++.|++++.+|+++|||||+|.++++|++|++ +++..+.|+.|.|.+|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999998 6999999999999876

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1.2e-17  Score=131.05  Aligned_cols=75  Identities=33%  Similarity=0.553  Sum_probs=70.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEE
Q 005812          427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLK  506 (676)
Q Consensus       427 ~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~  506 (676)
                      .|||+|||+++++++|+++|++||.|..+.|+.++.+++++|||||+|.++++|.+|++ ++     +..|+|+.|.|..
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~-----~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QK-----EHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TC-----CCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cC-----CCEECCCEEEeeE
Confidence            48999999999999999999999999999999999999999999999999999999997 67     8899999999976


Q ss_pred             c
Q 005812          507 A  507 (676)
Q Consensus       507 a  507 (676)
                      |
T Consensus        75 A   75 (75)
T d1hd0a_          75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=3.3e-17  Score=132.30  Aligned_cols=78  Identities=26%  Similarity=0.489  Sum_probs=72.6

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCC---CceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTG---LSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       219 v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~---~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      |||+|||+++++++|+++|++||.|.+|.|++++.++   .++|||||+|.+.++|.+|++.|||..++|+.|.|.|+.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999999876554   4689999999999999999999999999999999999865


Q ss_pred             C
Q 005812          296 K  296 (676)
Q Consensus       296 ~  296 (676)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            4

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.69  E-value=1.9e-17  Score=133.81  Aligned_cols=80  Identities=21%  Similarity=0.285  Sum_probs=70.4

Q ss_pred             CCeEEEcCCCCCCC-HHHHHHHHHhCCceeEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          425 QNTIFICNLPFDLD-NEEVKQRFSAFGEVVSFVPVLH-QVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       425 ~~~l~V~nLp~~~t-eedl~~~F~~~G~v~~v~i~~~-~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      +++|||+|||++++ +++|+++|++||.|.+|+|+.+ ..++.++|||||+|.+.++|.+|++ ||     +..|+|+.|
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n-----~~~~~gr~l   77 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MN-----RSLLGNREI   77 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GT-----TEEETTEEE
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cC-----CCEECCEEE
Confidence            57999999999986 5569999999999999998764 4688999999999999999999995 99     999999999


Q ss_pred             EEEEccCc
Q 005812          503 TVLKALDK  510 (676)
Q Consensus       503 ~v~~a~~k  510 (676)
                      .|.+|.++
T Consensus        78 ~V~~a~~k   85 (86)
T d2ghpa3          78 SVSLADKK   85 (86)
T ss_dssp             EEEECCCC
T ss_pred             EEEEcCCC
Confidence            99999875

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.8e-17  Score=139.36  Aligned_cols=82  Identities=32%  Similarity=0.574  Sum_probs=78.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      .++|||+|||+++++++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|..|++.|+|..|.|+.|.|.|+.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            46899999999999999999999999999999999998999999999999999999999999999999999999999876


Q ss_pred             CC
Q 005812          296 KN  297 (676)
Q Consensus       296 ~~  297 (676)
                      +.
T Consensus        88 ~~   89 (104)
T d1p1ta_          88 EK   89 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.1e-16  Score=131.41  Aligned_cols=84  Identities=35%  Similarity=0.519  Sum_probs=77.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+.+++++|+++|+.||.|.+|.++.+.  +.++|||||+|.+.++|.+|++.|||..|.|+.|+|.
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44566789999999999999999999999999999999875  3378999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.++.
T Consensus        85 ~A~~r~   90 (93)
T d2cq3a1          85 NATARV   90 (93)
T ss_dssp             ECCSSC
T ss_pred             ecCcCC
Confidence            998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=3e-17  Score=136.93  Aligned_cols=81  Identities=19%  Similarity=0.377  Sum_probs=77.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      .++|||+|||+++++++|+++|++||.|..+.|++++.++.++|||||+|.+.++|.+|++ +++..|.|+.|.|.++.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            3789999999999999999999999999999999999999999999999999999999997 799999999999999987


Q ss_pred             CC
Q 005812          296 KN  297 (676)
Q Consensus       296 ~~  297 (676)
                      +.
T Consensus        99 ke  100 (103)
T d1x4ba1          99 RE  100 (103)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=6.7e-17  Score=135.28  Aligned_cols=84  Identities=21%  Similarity=0.326  Sum_probs=77.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||+.+++++|+++|+.||.|.+|+|+.++.+|.++|||||+|.+.++|.+|++.+++ .|.|+.|.|.|
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~   85 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   85 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEE
Confidence            34457899999999999999999999999999999999999999999999999999999999998776 79999999999


Q ss_pred             ecCCC
Q 005812          293 AVPKN  297 (676)
Q Consensus       293 a~~~~  297 (676)
                      +.+..
T Consensus        86 a~~~~   90 (103)
T d2cqda1          86 AYLGA   90 (103)
T ss_dssp             STTTC
T ss_pred             cCCCC
Confidence            87543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=2.6e-17  Score=133.98  Aligned_cols=79  Identities=37%  Similarity=0.568  Sum_probs=74.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      .+|||+|||+.+++++|+++|+.||.|..++|+.+.  +.++|||||+|.+.++|++|++.||     |..|+|+.|.|.
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~-----g~~~~g~~i~V~   81 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMN-----GMLLNDRKVFVG   81 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSS-----EEEETTEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcC-----CCEECCEEEEEE
Confidence            589999999999999999999999999999999885  3468999999999999999999999     999999999999


Q ss_pred             EccCch
Q 005812          506 KALDKK  511 (676)
Q Consensus       506 ~a~~k~  511 (676)
                      +|.++.
T Consensus        82 ~a~~~~   87 (89)
T d1cvja2          82 RFKSRK   87 (89)
T ss_dssp             ECCCTT
T ss_pred             ECCCCC
Confidence            998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.69  E-value=7.4e-17  Score=143.38  Aligned_cols=84  Identities=25%  Similarity=0.395  Sum_probs=79.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++|||+|||+++++++|+++|+.||.|.+|.|++++.+|+++|||||+|.+.++|..|++.|||..|.|+.|+|.|+.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCCC
Q 005812          295 PKNI  298 (676)
Q Consensus       295 ~~~~  298 (676)
                      ++..
T Consensus       121 ~~~~  124 (139)
T d1u6fa1         121 SGHQ  124 (139)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=6.7e-17  Score=131.82  Aligned_cols=82  Identities=24%  Similarity=0.401  Sum_probs=75.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ...++|||+|||.++++++|+++|+.||.|.+|.++.+..+  .+|||||+|.+.++|..|++.|+|..|.|+.|+|.|+
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            45679999999999999999999999999999999988654  4799999999999999999999999999999999999


Q ss_pred             cCCC
Q 005812          294 VPKN  297 (676)
Q Consensus       294 ~~~~  297 (676)
                      .++.
T Consensus        84 ~~~~   87 (90)
T d2cqia1          84 TTPS   87 (90)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            7653

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=3.1e-17  Score=128.71  Aligned_cols=75  Identities=25%  Similarity=0.428  Sum_probs=71.2

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       218 ~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      +|||+|||+++++++|+++|++||.|.++.|++++.+++++|||||+|.++++|++|++ +++..|.|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            48999999999999999999999999999999999999999999999999999999998 7999999999998643

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=8.2e-17  Score=127.97  Aligned_cols=77  Identities=19%  Similarity=0.361  Sum_probs=73.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      ++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.++++|.+|+ .++     +..|+||.|.|.
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al-~~~-----~~~l~Gr~i~V~   76 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQK-----YHTVNGHNCEVR   76 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCS-----CCEETTEECEEE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhC-----CCEECCEEEEEE
Confidence            68999999999999999999999999999999999999999999999999999999998 589     999999999999


Q ss_pred             Ecc
Q 005812          506 KAL  508 (676)
Q Consensus       506 ~a~  508 (676)
                      +|.
T Consensus        77 ~A~   79 (79)
T d1l3ka2          77 KAL   79 (79)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            873

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.9e-17  Score=136.61  Aligned_cols=80  Identities=26%  Similarity=0.399  Sum_probs=76.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      .++|||+|||+++++++|+++|+.||.|.+|+|+++..+|.++|||||+|.+.++|.+|+. |||..|.|+.|.|.++.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            4789999999999999999999999999999999999999999999999999999999996 999999999999999865


Q ss_pred             C
Q 005812          296 K  296 (676)
Q Consensus       296 ~  296 (676)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            3

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=4.8e-17  Score=139.33  Aligned_cols=80  Identities=21%  Similarity=0.375  Sum_probs=73.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      .+++|||+|||+.+++++|+++|++||.|.+|++..+   +.++|||||+|.+.++|..|++.||     |..|+|++|.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~-----g~~~~gr~l~   77 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLS-----GFNVCNRYLV   77 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHT-----TCEETTEECE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhC-----CCEECCEEEE
Confidence            4689999999999999999999999999999988754   5679999999999999999999999     9999999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.++.++.
T Consensus        78 V~~a~~~~   85 (114)
T d2f9da1          78 VLYYNANR   85 (114)
T ss_dssp             EEECCHHH
T ss_pred             EEEcCCCc
Confidence            99987543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.67  E-value=5.3e-17  Score=131.11  Aligned_cols=81  Identities=28%  Similarity=0.443  Sum_probs=71.3

Q ss_pred             CCcEEEEcCCCCCCC-HHHHHHhhccCCceEEEEEccc-CCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          215 QKWKLIIRNIPFKAK-VNEIKDMFSPVGLVWNVYIPHN-TDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~-e~~l~~~F~~~G~i~~v~i~~~-~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ..++|||+|||++++ +++|+++|++||.|.+|+|+.+ ..+++++|||||+|.+.++|.+|++ |||..|.|+.|+|.|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            467999999999976 5669999999999999998764 4678999999999999999999996 999999999999999


Q ss_pred             ecCC
Q 005812          293 AVPK  296 (676)
Q Consensus       293 a~~~  296 (676)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=1.2e-16  Score=132.89  Aligned_cols=86  Identities=27%  Similarity=0.426  Sum_probs=79.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhC------CceeCC
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN------GQKFGK  285 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~------~~~~~g  285 (676)
                      .....++|||+|||+++++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+|++.|+      |..+.|
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            34456899999999999999999999999999999999999899999999999999999999999886      667899


Q ss_pred             eeEEEEEecCCC
Q 005812          286 RPIAVDWAVPKN  297 (676)
Q Consensus       286 ~~i~v~~a~~~~  297 (676)
                      +.|.|.|+.++.
T Consensus        84 r~l~v~~a~~k~   95 (98)
T d1x4ha1          84 RQLKVDLAVTRD   95 (98)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEEECCCCC
Confidence            999999998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.6e-17  Score=139.35  Aligned_cols=86  Identities=23%  Similarity=0.306  Sum_probs=80.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ...++++|||+|||..+++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|++.||     |..|.|+
T Consensus        14 ~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~-----g~~~~g~   88 (102)
T d2cpxa1          14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVN-----GYKLYGK   88 (102)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHST-----TCBCSSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhC-----CCEECCE
Confidence            34467899999999999999999999999999999888887789999999999999999999999999     9999999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      +|.|.||.++.
T Consensus        89 ~l~V~~ak~k~   99 (102)
T d2cpxa1          89 ILVIEFGKNKK   99 (102)
T ss_dssp             BCEEEECCCCS
T ss_pred             EEEEEeCCCcc
Confidence            99999998865

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.4e-16  Score=126.58  Aligned_cols=77  Identities=19%  Similarity=0.284  Sum_probs=73.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      .++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++ ++|..|.|+.|.|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            3689999999999999999999999999999999999999999999999999999999997 7999999999999876

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=6.6e-17  Score=131.55  Aligned_cols=80  Identities=26%  Similarity=0.402  Sum_probs=74.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecC
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVP  295 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~  295 (676)
                      ..+|||+|||+++++++|+++|+.||.|.++.|+.+.  +.++|||||+|.+.++|++|++.|||..|.|+.|.|.++.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4579999999999999999999999999999999885  34789999999999999999999999999999999999987


Q ss_pred             CC
Q 005812          296 KN  297 (676)
Q Consensus       296 ~~  297 (676)
                      +.
T Consensus        86 ~~   87 (89)
T d1cvja2          86 RK   87 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=2.5e-17  Score=128.77  Aligned_cols=75  Identities=25%  Similarity=0.346  Sum_probs=70.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEE
Q 005812          427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLK  506 (676)
Q Consensus       427 ~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~  506 (676)
                      .|||+|||+++|+++|+++|++||.|..|+|++++.++.++|||||+|.+.++|.+|++. +     +..|+|+.|.|..
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~-----~~~i~g~~i~vk~   74 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-K-----YHNVGLSKCEIKV   74 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-S-----SCCBTTBCCEEEC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-C-----CCEECCEEeEEEE
Confidence            489999999999999999999999999999999999999999999999999999999965 5     6789999999976


Q ss_pred             c
Q 005812          507 A  507 (676)
Q Consensus       507 a  507 (676)
                      |
T Consensus        75 A   75 (75)
T d1x0fa1          75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            5

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=7.8e-17  Score=134.83  Aligned_cols=84  Identities=24%  Similarity=0.282  Sum_probs=76.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCcee--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCC
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVV--------SFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLG  494 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~--------~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g  494 (676)
                      ...++|||+|||+.+++++|+++|+.||.|.        .+.+..+..++.++|||||+|.++++|.+|++.||     |
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~-----g   80 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFD-----G   80 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHT-----T
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhC-----C
Confidence            3468999999999999999999999999874        46677777889999999999999999999999999     9


Q ss_pred             eeecCcEEEEEEccCch
Q 005812          495 IFLKGRQLTVLKALDKK  511 (676)
Q Consensus       495 ~~l~gr~l~v~~a~~k~  511 (676)
                      ..|+||.|.|.+|.++.
T Consensus        81 ~~~~gr~i~V~~a~~~~   97 (101)
T d2cpea1          81 KDFQGSKLKVSLARKKP   97 (101)
T ss_dssp             CEETTEECEEECSSCCC
T ss_pred             CEECCEEEEEEEcCCCC
Confidence            99999999999998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=5.3e-17  Score=127.77  Aligned_cols=75  Identities=24%  Similarity=0.405  Sum_probs=71.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEE
Q 005812          427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLK  506 (676)
Q Consensus       427 ~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~  506 (676)
                      .|||+|||+++|+++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|.+|++ +|     +..|+||+|.|.+
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~-----~~~l~gr~i~V~~   74 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IH-----FHEINNKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CS-----SCCBTTBCCEEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cC-----CCEECCeEEEEEE
Confidence            48999999999999999999999999999999998899999999999999999999996 99     9999999999988


Q ss_pred             c
Q 005812          507 A  507 (676)
Q Consensus       507 a  507 (676)
                      |
T Consensus        75 A   75 (75)
T d2msta_          75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            6

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=2.2e-16  Score=132.08  Aligned_cols=86  Identities=22%  Similarity=0.362  Sum_probs=78.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceE--------EEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVW--------NVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF  283 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~--------~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  283 (676)
                      .....++|||+|||..+++++|+++|+.||.|.        .+.+..++.+|+++|||||+|.++++|..|++.|||..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            345678999999999999999999999999874        567778888899999999999999999999999999999


Q ss_pred             CCeeEEEEEecCCC
Q 005812          284 GKRPIAVDWAVPKN  297 (676)
Q Consensus       284 ~g~~i~v~~a~~~~  297 (676)
                      .|+.|+|.|+.++.
T Consensus        84 ~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 QGSKLKVSLARKKP   97 (101)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=3.6e-17  Score=127.84  Aligned_cols=75  Identities=19%  Similarity=0.387  Sum_probs=70.9

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       218 ~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      +|||+|||+++|+++|+++|++||.|.+|.|+.++.+++++|||||+|.+.++|++||+. ++..+.|+.|.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            589999999999999999999999999999999999999999999999999999999984 788899999998764

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.6e-16  Score=130.87  Aligned_cols=76  Identities=22%  Similarity=0.424  Sum_probs=71.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||..+++++|+++|++||.|.+|+++++      +|||||+|.+.++|.+|+..||     |..|+|+.|+|
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~-----~~~i~g~~l~v   86 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVN-----GTTIEGHVVKC   86 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHT-----TCEETTEECEE
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhC-----CCEECCEEEEE
Confidence            478999999999999999999999999999998855      7899999999999999999999     99999999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .|++++.
T Consensus        87 ~~ak~~p   93 (96)
T d1x4ga1          87 YWGKESP   93 (96)
T ss_dssp             ECCCCCC
T ss_pred             EEcCCCC
Confidence            9987753

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.65  E-value=2.7e-17  Score=134.21  Aligned_cols=80  Identities=20%  Similarity=0.230  Sum_probs=73.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      ...+|||+|||+++++++|+++|+.||.|..+.|+.+ .+|+++|||||+|.+.++|.+||+ ||     +..|+|++|.
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~-----g~~~~g~~i~   84 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LT-----GLKVFGNEIK   84 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GG-----GEEETTEEEE
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cC-----CcEECCEEEE
Confidence            4579999999999999999999999999999877654 678999999999999999999995 99     9999999999


Q ss_pred             EEEccCc
Q 005812          504 VLKALDK  510 (676)
Q Consensus       504 v~~a~~k  510 (676)
                      |.+|.+|
T Consensus        85 V~~ak~k   91 (91)
T d1fjeb1          85 LEKPKGR   91 (91)
T ss_dssp             EECCCCS
T ss_pred             EEecCCC
Confidence            9998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=1.1e-16  Score=125.98  Aligned_cols=75  Identities=19%  Similarity=0.371  Sum_probs=72.1

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          218 KLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       218 ~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      +|||+|||+++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|++|++ +||..|.|+.|+|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            48999999999999999999999999999999999899999999999999999999997 8999999999999875

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.6e-16  Score=134.65  Aligned_cols=80  Identities=24%  Similarity=0.382  Sum_probs=73.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ..+++|||+|||..+++++|+++|+.||.|.+|++..+   +.++|||||+|.+.++|..|++.|||..|.|+.|.|.|+
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            35679999999999999999999999999999999864   557899999999999999999999999999999999998


Q ss_pred             cCC
Q 005812          294 VPK  296 (676)
Q Consensus       294 ~~~  296 (676)
                      .+.
T Consensus        82 ~~~   84 (114)
T d2f9da1          82 NAN   84 (114)
T ss_dssp             CHH
T ss_pred             CCC
Confidence            653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=9.3e-17  Score=132.73  Aligned_cols=84  Identities=21%  Similarity=0.230  Sum_probs=74.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCc-eeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGE-VVSFVPVLHQ-VTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~-v~~v~i~~~~-~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      ++|||+|||..+++++|+++|+.||. |..++++++. .+++++|||||+|.++++|.+|++.|+..   ++.++|++|.
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~---~~~~~g~~i~   78 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPG---RIQLWGHQIA   78 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTC---CSCBTTBCCE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCC---CeEECCEEEE
Confidence            68999999999999999999999995 8999888875 46889999999999999999999999622   6777899999


Q ss_pred             EEEccCchh
Q 005812          504 VLKALDKKL  512 (676)
Q Consensus       504 v~~a~~k~~  512 (676)
                      |.||.++..
T Consensus        79 V~~A~p~~~   87 (96)
T d2disa1          79 VDWAEPEID   87 (96)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=4.4e-16  Score=125.16  Aligned_cols=76  Identities=24%  Similarity=0.367  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+++|+++|+++|+.||.|..|+++.+ .++.++|||||+|.++++|.+|++ ++     +..+.|+.|.|
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~-~~~~~kG~afV~f~~~e~a~~al~-~~-----~~~~~g~~l~v   78 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE-TP-----GQKYKETDLLI   78 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC-TTCCEEEEEEEEESCHHHHHHHHT-CC-----CCEETTEECEE
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee-ccCCcceEEEEEEcCHHHHHHHHH-HC-----CCEECCEEEEE
Confidence            479999999999999999999999999999988776 478999999999999999999995 68     99999999999


Q ss_pred             EEc
Q 005812          505 LKA  507 (676)
Q Consensus       505 ~~a  507 (676)
                      .++
T Consensus        79 ~~~   81 (85)
T d1zh5a2          79 LFK   81 (85)
T ss_dssp             EEG
T ss_pred             EEc
Confidence            985

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=3.6e-16  Score=126.02  Aligned_cols=78  Identities=24%  Similarity=0.456  Sum_probs=72.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ...++|||+|||.++++++|+++|++||.|.+|.+.++      +|||||+|.+.++|..|++.|||..|.|+.|+|.||
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A   79 (86)
T d2cpja1           6 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   79 (86)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            35578999999999999999999999999999999864      589999999999999999999999999999999999


Q ss_pred             cCCC
Q 005812          294 VPKN  297 (676)
Q Consensus       294 ~~~~  297 (676)
                      .+..
T Consensus        80 ~~~~   83 (86)
T d2cpja1          80 CHSA   83 (86)
T ss_dssp             SCCS
T ss_pred             CCcC
Confidence            7654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=3.5e-16  Score=128.88  Aligned_cols=80  Identities=20%  Similarity=0.290  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .++++|||+|||+.+++++|+++|+.||.|..+.+..+   +.++|||||+|.+.++|..|++.||     +..|.|++|
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~-----g~~~~g~~l   83 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRD-----GYDYDGYRL   83 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHT-----TCEETTEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhC-----CCEECCEEE
Confidence            34578999999999999999999999999999876543   4568999999999999999999999     999999999


Q ss_pred             EEEEccCc
Q 005812          503 TVLKALDK  510 (676)
Q Consensus       503 ~v~~a~~k  510 (676)
                      .|.||++.
T Consensus        84 ~V~~a~~~   91 (95)
T d1x4aa1          84 RVEFPRSG   91 (95)
T ss_dssp             EEECCCCC
T ss_pred             EEEeccCC
Confidence            99998753

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=5.7e-16  Score=124.50  Aligned_cols=78  Identities=22%  Similarity=0.362  Sum_probs=72.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++|||+|||.++++++|+++|+.||.|..|.|+.+. +|.++|||||+|.++++|++|++ +++..+.|+.|.|.|..
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            35789999999999999999999999999999998875 78899999999999999999997 69999999999999863

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=8.2e-17  Score=134.93  Aligned_cols=85  Identities=20%  Similarity=0.252  Sum_probs=79.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      .++++|||+|||..+++++|+++|+.||.|..+.+..+..+|+++|||||+|.+.++|..|++.|||..|.|+.|+|.|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45689999999999999999999999999999998888778999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 005812          294 VPKNI  298 (676)
Q Consensus       294 ~~~~~  298 (676)
                      .++..
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            87653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=2.9e-16  Score=130.91  Aligned_cols=82  Identities=26%  Similarity=0.466  Sum_probs=75.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      ....++|||+|||+++++++|+++|+.||.|..+.+..+. ++.++|||||+|.+.++|++|++.|||..|.|+++.|.+
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            3456799999999999999999999999999999988874 788999999999999999999999999999999999988


Q ss_pred             ecC
Q 005812          293 AVP  295 (676)
Q Consensus       293 a~~  295 (676)
                      +.|
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            765

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=7.1e-16  Score=126.98  Aligned_cols=82  Identities=22%  Similarity=0.419  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+++++++|+++|+.||.|..+.+..+   +.++|||||+|.+.++|..|++.|||..|.|+.|.|+
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~   86 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   86 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456679999999999999999999999999999988664   4478999999999999999999999999999999999


Q ss_pred             EecCC
Q 005812          292 WAVPK  296 (676)
Q Consensus       292 ~a~~~  296 (676)
                      |+.+.
T Consensus        87 ~a~~~   91 (95)
T d1x4aa1          87 FPRSG   91 (95)
T ss_dssp             CCCCC
T ss_pred             eccCC
Confidence            98654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=2.4e-16  Score=127.43  Aligned_cols=78  Identities=21%  Similarity=0.306  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      ..+|||+|||++++++||+++|+.||.+....++.+..++.++|+|||+|.+.++|.+|+..||     +..|+||+|.|
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~-----~~~l~gr~i~v   83 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLN-----DRPIGSRKVKL   83 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTT-----TCEETTEECEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcC-----CCEECCEEEEE
Confidence            3679999999999999999999999998774445555689999999999999999999999999     99999999999


Q ss_pred             EEc
Q 005812          505 LKA  507 (676)
Q Consensus       505 ~~a  507 (676)
                      .++
T Consensus        84 ~l~   86 (86)
T d2cqpa1          84 VLG   86 (86)
T ss_dssp             EES
T ss_pred             EEC
Confidence            875

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.63  E-value=6.7e-16  Score=123.67  Aligned_cols=78  Identities=19%  Similarity=0.293  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee-CCeeEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF-GKRPIAV  290 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~-~g~~i~v  290 (676)
                      ..+++++|||+|||.++++++|+++|+.||.|.+|+++++     .+|||||+|.+.++|..|++.|+|..| .|+.|+|
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v   78 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKI   78 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEE
Confidence            3455789999999999999999999999999999999875     468999999999999999999999988 5689999


Q ss_pred             EEec
Q 005812          291 DWAV  294 (676)
Q Consensus       291 ~~a~  294 (676)
                      .||+
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9985

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.63  E-value=3.5e-16  Score=125.32  Aligned_cols=78  Identities=21%  Similarity=0.270  Sum_probs=70.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee-cC
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL-KG  499 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l-~g  499 (676)
                      ..+|+++|||+|||..+++++|+++|+.||.|..|+++++     .+|||||+|.+.++|..|+..|+     |..| +|
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~-----g~~~~~~   73 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQ-----GFKITPT   73 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHT-----TCBSSTT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhC-----CcEeCCC
Confidence            3445789999999999999999999999999999988754     36899999999999999999999     8888 47


Q ss_pred             cEEEEEEcc
Q 005812          500 RQLTVLKAL  508 (676)
Q Consensus       500 r~l~v~~a~  508 (676)
                      ++|.|.||+
T Consensus        74 ~~i~v~~ak   82 (83)
T d2b0ga1          74 HAMKITFAK   82 (83)
T ss_dssp             CBCEEEECC
T ss_pred             cEEEEEEec
Confidence            899999985

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=4.9e-16  Score=127.92  Aligned_cols=78  Identities=21%  Similarity=0.394  Sum_probs=72.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ...++|||+|||..+++++|+++|++||.|.+|+|+++      +|||||+|.+.++|..|+..|+|..|.|+.|+|.|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34578999999999999999999999999999999874      689999999999999999999999999999999999


Q ss_pred             cCCC
Q 005812          294 VPKN  297 (676)
Q Consensus       294 ~~~~  297 (676)
                      +++.
T Consensus        90 k~~p   93 (96)
T d1x4ga1          90 KESP   93 (96)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=2.1e-16  Score=131.81  Aligned_cols=79  Identities=23%  Similarity=0.450  Sum_probs=73.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+++++++|+++|+.||.|..+.++.+ .++.++|||||+|.+.++|.+|++.||     |..|.||++.|
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~ln-----g~~i~gr~~~v   91 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFN-----GKFIKTPPGVS   91 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHB-----TCCCCCCTTSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhC-----CCEECCcCCcc
Confidence            478999999999999999999999999999988877 478899999999999999999999999     99999999998


Q ss_pred             EEccC
Q 005812          505 LKALD  509 (676)
Q Consensus       505 ~~a~~  509 (676)
                      .++.|
T Consensus        92 ~~~~P   96 (101)
T d1x5oa1          92 APTEP   96 (101)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            77654

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=2e-16  Score=125.66  Aligned_cols=75  Identities=23%  Similarity=0.314  Sum_probs=68.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCe-eecCcEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGI-FLKGRQLTV  504 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~-~l~gr~l~v  504 (676)
                      ++|||+|||+++++++|+++|++||.|..+.++.      ++|||||+|.++++|.+|++.||     |. .++|++|.|
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~ln-----g~~~~~G~~i~V   70 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLS-----GKVELHGKIMEV   70 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHT-----TTCEETTEECEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhC-----CCeEECCEEEEE
Confidence            4799999999999999999999999998876654      37899999999999999999999     85 699999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .||.++.
T Consensus        71 ~~a~~k~   77 (80)
T d2cqha1          71 DYSVSKK   77 (80)
T ss_dssp             EECCCCC
T ss_pred             EEcCCcC
Confidence            9999864

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=6e-16  Score=127.78  Aligned_cols=83  Identities=33%  Similarity=0.437  Sum_probs=74.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCc-eEEEEEcccC-CCCCceeEEEEEecCHHHHHHHHHHhCCc--eeCCeeEEEE
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGL-VWNVYIPHNT-DTGLSKGFAFVKFTCKRDAESAIQKFNGQ--KFGKRPIAVD  291 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~-i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~~~--~~~g~~i~v~  291 (676)
                      +++|||+|||..+++++|+++|+.||. |.++.++.+. .+++++|||||+|.+.++|..|++.|++.  .++|+.|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            468999999999999999999999996 9999999875 36889999999999999999999998654  5579999999


Q ss_pred             EecCCCC
Q 005812          292 WAVPKNI  298 (676)
Q Consensus       292 ~a~~~~~  298 (676)
                      ||.|+..
T Consensus        81 ~A~p~~~   87 (96)
T d2disa1          81 WAEPEID   87 (96)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9987653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=5.2e-16  Score=125.40  Aligned_cols=81  Identities=22%  Similarity=0.403  Sum_probs=72.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      .+...+|||+|||+++++++|+++|+.||.|....++.+..++.++|||||+|.+.++|++|++.||+..+.|++|+|.+
T Consensus         6 ~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           6 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567899999999999999999999999987644444446899999999999999999999999999999999999987


Q ss_pred             e
Q 005812          293 A  293 (676)
Q Consensus       293 a  293 (676)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.62  E-value=6.5e-16  Score=127.48  Aligned_cols=78  Identities=22%  Similarity=0.391  Sum_probs=71.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      +.++|||+|||+++++++|+++|++||.|..+.     .++.++|||||+|.+.++|.+|+..||     +..|+||+|.
T Consensus        15 ~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~-----~~~~~gr~i~   84 (96)
T d1fjca_          15 AARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQ-----GAEIDGRSVS   84 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTT-----EEEETTEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcC-----CCEECCEEEE
Confidence            458999999999999999999999999887664     257789999999999999999999999     9999999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.|+.++.
T Consensus        85 V~~a~~k~   92 (96)
T d1fjca_          85 LYYTGEKG   92 (96)
T ss_dssp             EEECSSSC
T ss_pred             EEEeCCCC
Confidence            99998864

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=1.4e-15  Score=122.72  Aligned_cols=76  Identities=20%  Similarity=0.267  Sum_probs=69.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||+.+++++|+++|++||.|..+.+.      .++|||||+|.++++|.+|+..||     |..|+|+.|.|
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~-----~~~i~g~~i~V   76 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALN-----GKVLDGSPIEV   76 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHS-----SEEETTEEEEE
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcC-----CCEECCEEEEE
Confidence            4789999999999999999999999998887653      358899999999999999999999     99999999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .||+|++
T Consensus        77 ~~akP~~   83 (86)
T d2cpda1          77 TLAKPVD   83 (86)
T ss_dssp             ECCCCCC
T ss_pred             EeccCCC
Confidence            9998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=6.8e-16  Score=122.27  Aligned_cols=77  Identities=18%  Similarity=0.302  Sum_probs=70.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      +...++|||+|||  +|+++|+++|++||.|.+|.+.+      .+|||||+|.+.++|..|+..|||..+.|+.|+|.|
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   73 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   73 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET------TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeecc------CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456799999996  89999999999999999999976      458999999999999999999999999999999999


Q ss_pred             ecCCC
Q 005812          293 AVPKN  297 (676)
Q Consensus       293 a~~~~  297 (676)
                      +.++.
T Consensus        74 a~~~P   78 (79)
T d2bz2a1          74 ARKQP   78 (79)
T ss_dssp             CCSSC
T ss_pred             ecCCC
Confidence            97653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=4.3e-16  Score=126.39  Aligned_cols=76  Identities=22%  Similarity=0.409  Sum_probs=69.4

Q ss_pred             CCeEEEcCCCCCCCHHHH---HHHHHhCCceeEEEEeecCCCCC---cceEEEEEeCCHHHHHHHHHHcCCCCCCCeeec
Q 005812          425 QNTIFICNLPFDLDNEEV---KQRFSAFGEVVSFVPVLHQVTKR---PKGTGFLKFKTVEAATAAVSASKTTSGLGIFLK  498 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl---~~~F~~~G~v~~v~i~~~~~~~~---~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~  498 (676)
                      .++|||+|||+.+++++|   .++|++||.|..|.+++++.++.   .+|||||+|.++++|.+|++.||     |..|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~ln-----g~~~~   82 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVN-----NVVVD   82 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHT-----TEEET
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhC-----CCEEC
Confidence            468999999999999999   77899999999999998876554   45999999999999999999999     99999


Q ss_pred             CcEEEEE
Q 005812          499 GRQLTVL  505 (676)
Q Consensus       499 gr~l~v~  505 (676)
                      ||+|+|+
T Consensus        83 gr~lkvS   89 (89)
T d2cpia1          83 GRTLKAS   89 (89)
T ss_dssp             TEEEEEE
T ss_pred             CEEEEEC
Confidence            9999985

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=1.2e-15  Score=123.23  Aligned_cols=77  Identities=25%  Similarity=0.371  Sum_probs=71.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++|||+|||+.+++++|+++|+.||.|..+.+..      ++|||||+|.+.++|..|+..|||..|.|+.|.|.|+.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            457899999999999999999999999988777754      67999999999999999999999999999999999998


Q ss_pred             CCC
Q 005812          295 PKN  297 (676)
Q Consensus       295 ~~~  297 (676)
                      |+.
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=5.1e-16  Score=125.09  Aligned_cols=75  Identities=29%  Similarity=0.464  Sum_probs=70.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      .++|||+|||.++++++|+++|++||.|.+|+++++      +|||||+|.+.++|.+|+..||     |..|+|++|.|
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~-----g~~i~g~~l~V   76 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELD-----NMPLRGKQLRV   76 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHT-----TCCBTTBCCEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhC-----CCEECCEEEEE
Confidence            368999999999999999999999999999988644      6899999999999999999999     99999999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      .||.++
T Consensus        77 ~~A~~~   82 (86)
T d2cpja1          77 RFACHS   82 (86)
T ss_dssp             EESSCC
T ss_pred             EECCCc
Confidence            998765

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=2.4e-16  Score=125.18  Aligned_cols=75  Identities=24%  Similarity=0.395  Sum_probs=68.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCc-eeCCeeEEEEEecC
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQ-KFGKRPIAVDWAVP  295 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~-~~~g~~i~v~~a~~  295 (676)
                      .+|||+|||.++++++|+++|++||.|.++.+..      ++|||||+|.+.++|.+|++.|||. .+.|+.|.|+|+.|
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4799999999999999999999999988776665      5799999999999999999999996 69999999999988


Q ss_pred             CC
Q 005812          296 KN  297 (676)
Q Consensus       296 ~~  297 (676)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            65

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.61  E-value=7.2e-17  Score=131.57  Aligned_cols=83  Identities=23%  Similarity=0.308  Sum_probs=75.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      ......+|||+|||+++++++|+++|+.||.|..+.|+.+ .+|+++|||||+|.+.++|++||+ |||..+.|+.|.|.
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEE
Confidence            3456679999999999999999999999999998888654 588999999999999999999996 89999999999999


Q ss_pred             EecCC
Q 005812          292 WAVPK  296 (676)
Q Consensus       292 ~a~~~  296 (676)
                      +++.+
T Consensus        87 ~ak~k   91 (91)
T d1fjeb1          87 KPKGR   91 (91)
T ss_dssp             CCCCS
T ss_pred             ecCCC
Confidence            98653

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=3.5e-16  Score=132.99  Aligned_cols=89  Identities=19%  Similarity=0.322  Sum_probs=78.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ...+++|||+|||+++|+++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|++|+. ||     +..|+||.
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~-----~~~i~gR~   88 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RH-----KQYMGNRF   88 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SC-----SBCSTTSC
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cC-----CCcCCCEE
Confidence            3356799999999999999999999999999876677777789999999999999999999995 89     99999999


Q ss_pred             EEEEEccCchhhhhH
Q 005812          502 LTVLKALDKKLAHDK  516 (676)
Q Consensus       502 l~v~~a~~k~~~~~~  516 (676)
                      |.|.++.++......
T Consensus        89 i~V~~~~~~~~~~~~  103 (112)
T d1wela1          89 IQVHPITKKGMLEKI  103 (112)
T ss_dssp             BEEEEECHHHHHHHH
T ss_pred             EEEEEcChHHHHHHH
Confidence            999998776654433

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=2.8e-16  Score=122.34  Aligned_cols=71  Identities=18%  Similarity=0.301  Sum_probs=68.4

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEE
Q 005812          219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIA  289 (676)
Q Consensus       219 v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~  289 (676)
                      |||+|||.++++++|+++|++||.|..+++.+++.++.++|||||+|.+.++|++|++.|||..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999999999999999999999999999999999999998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=7.1e-16  Score=125.09  Aligned_cols=78  Identities=22%  Similarity=0.261  Sum_probs=70.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHH---HHhhccCCceEEEEEcccCCCCC---ceeEEEEEecCHHHHHHHHHHhCCceeCCee
Q 005812          214 TQKWKLIIRNIPFKAKVNEI---KDMFSPVGLVWNVYIPHNTDTGL---SKGFAFVKFTCKRDAESAIQKFNGQKFGKRP  287 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l---~~~F~~~G~i~~v~i~~~~~~~~---~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  287 (676)
                      ...++|||+|||+++++++|   +++|++||.|.+|.|++++.++.   .+|||||+|.+.++|.+|++.|||..|.|+.
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            34568999999999999999   67899999999999998876654   4599999999999999999999999999999


Q ss_pred             EEEE
Q 005812          288 IAVD  291 (676)
Q Consensus       288 i~v~  291 (676)
                      |+|.
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9984

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=8.8e-16  Score=124.56  Aligned_cols=78  Identities=22%  Similarity=0.296  Sum_probs=69.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee-cCcEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL-KGRQL  502 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l-~gr~l  502 (676)
                      |+++|||+|||+++++++|+++|+.||.|..+.++..    ..+|||||+|.+.++|.+|+..|+     |..| +|++|
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~-----~~~i~~g~~l   79 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLH-----NHDLGENHHL   79 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHT-----TCBSSSSCBC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhcc-----CCEecCCCEE
Confidence            4689999999999999999999999999988766543    357899999999999999999999     8888 58999


Q ss_pred             EEEEccCc
Q 005812          503 TVLKALDK  510 (676)
Q Consensus       503 ~v~~a~~k  510 (676)
                      +|.|++++
T Consensus        80 ~v~~sk~~   87 (88)
T d2adca2          80 RVSFSKST   87 (88)
T ss_dssp             EEEECSSC
T ss_pred             EEEeCCCC
Confidence            99998753

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

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

Probab=99.60  E-value=1.3e-15  Score=127.86  Aligned_cols=81  Identities=22%  Similarity=0.356  Sum_probs=71.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQ-VTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~-~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      +.++|||+|||+++++++|+++|+.|| +..++++.+. .++.++|||||+|.+.++|++|+ .||     +..|+||.|
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~-----~~~~~gr~l   86 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLN-----EESLGNKRI   86 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGG-----TCEETTEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcC-----CCEECCEEE
Confidence            458999999999999999999999999 7777777765 46789999999999999998776 699     999999999


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.+|.++.
T Consensus        87 ~V~~a~~~~   95 (104)
T d1wi8a_          87 RVDVADQAQ   95 (104)
T ss_dssp             EEEECCCCC
T ss_pred             EEEECCCCC
Confidence            999988753

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=6e-16  Score=122.61  Aligned_cols=74  Identities=23%  Similarity=0.401  Sum_probs=68.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      .+++|||+|+|  +|+++|+++|++||.|..+.+.+      .+|||||+|.+.++|..|+..||     |..++|++|+
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~------~~~~afV~f~~~~~A~~Ai~~ln-----g~~~~g~~l~   70 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVAELN-----GTQVESVQLK   70 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET------TTTEEEEECSSHHHHHHHHHHHT-----TCBCSSCBCE
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeecc------CCCEEEEEEcccHHHHHHHHHhC-----CCEECCEEEE
Confidence            35899999996  89999999999999999998753      36899999999999999999999     9999999999


Q ss_pred             EEEccCc
Q 005812          504 VLKALDK  510 (676)
Q Consensus       504 v~~a~~k  510 (676)
                      |.||+++
T Consensus        71 V~~a~~~   77 (79)
T d2bz2a1          71 VNIARKQ   77 (79)
T ss_dssp             EEECCSS
T ss_pred             EEEecCC
Confidence            9999765

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=8.8e-16  Score=128.72  Aligned_cols=82  Identities=22%  Similarity=0.301  Sum_probs=74.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          424 LQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      ...+|||+|||+++|++||+++|+.||.+..+.++.+..++.++|||||+|.++++|++|++ +|     +..|+||.|.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~-----~~~i~gR~i~   87 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KH-----KERIGHRYIE   87 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TT-----TCCSSSSCCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hC-----CCEEcceEEE
Confidence            34689999999999999999999999999887777777789999999999999999999995 88     8999999999


Q ss_pred             EEEccCch
Q 005812          504 VLKALDKK  511 (676)
Q Consensus       504 v~~a~~k~  511 (676)
                      |.++.+++
T Consensus        88 V~~~~~~~   95 (104)
T d1wg5a_          88 IFKSSRAE   95 (104)
T ss_dssp             EEEECTTT
T ss_pred             EEECCHHH
Confidence            99987653

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=4.5e-16  Score=127.08  Aligned_cols=80  Identities=26%  Similarity=0.446  Sum_probs=71.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHH----HHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          424 LQNTIFICNLPFDLDNEEVK----QRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       424 ~~~~l~V~nLp~~~teedl~----~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      |+++|||+|||+.++++||+    ++|++||.|.+|++..   ++.++|||||+|.+.++|.+|++.||     |..++|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~-----~~~~~g   73 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQ-----GFPFYD   73 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHT-----TCEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhC-----CCEECC
Confidence            35899999999999999886    4689999999987654   35679999999999999999999999     999999


Q ss_pred             cEEEEEEccCch
Q 005812          500 RQLTVLKALDKK  511 (676)
Q Consensus       500 r~l~v~~a~~k~  511 (676)
                      +.|.|.||.++.
T Consensus        74 ~~l~v~~ak~~~   85 (91)
T d1nu4a_          74 KPMRIQYAKTDS   85 (91)
T ss_dssp             EECEEEECSSCC
T ss_pred             EEEEEEEeCCCc
Confidence            999999998764

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=3.2e-15  Score=125.24  Aligned_cols=85  Identities=26%  Similarity=0.319  Sum_probs=77.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      .....+|||+|||+++++++|+++|..+|.|..+.++.+..++.++|||||+|.++++|++|++ +|+..|.|+.|.|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            4456689999999999999999999999999887777777789999999999999999999997 899999999999999


Q ss_pred             ecCCCC
Q 005812          293 AVPKNI  298 (676)
Q Consensus       293 a~~~~~  298 (676)
                      +.+...
T Consensus        91 ~~~~~~   96 (104)
T d1wg5a_          91 SSRAEV   96 (104)
T ss_dssp             ECTTTS
T ss_pred             CCHHHh
Confidence            987654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.60  E-value=1.7e-15  Score=118.37  Aligned_cols=74  Identities=16%  Similarity=0.221  Sum_probs=67.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      .+|||+|||+.+++++|+++|+.||.|..|+++.++.  ..++||||+|.++++|.+|+ .++     +..|+|++|.|.
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al-~~~-----~~~i~g~~i~V~   72 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAI-TKT-----HKVVGQNEIIVS   72 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHH-TTT-----TCEETTEECEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHH-Hhc-----CcEECCEEEEEE
Confidence            3899999999999999999999999999999988864  34689999999999999998 588     899999999998


Q ss_pred             Ec
Q 005812          506 KA  507 (676)
Q Consensus       506 ~a  507 (676)
                      .+
T Consensus        73 ~~   74 (75)
T d2ghpa2          73 HL   74 (75)
T ss_dssp             EC
T ss_pred             EC
Confidence            74

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=1.2e-15  Score=129.87  Aligned_cols=77  Identities=26%  Similarity=0.398  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ...++|||+|||+++++++|+++|+.||.|..|.|..      ++|||||+|.+.++|.+|++.|||..|.|+.|.|+|+
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a   81 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEEC
Confidence            3567999999999999999999999999999998864      5789999999999999999999999999999999999


Q ss_pred             cCC
Q 005812          294 VPK  296 (676)
Q Consensus       294 ~~~  296 (676)
                      ...
T Consensus        82 ~~~   84 (111)
T d1whxa_          82 PIG   84 (111)
T ss_dssp             ETT
T ss_pred             CCC
Confidence            654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=2.2e-16  Score=122.95  Aligned_cols=70  Identities=26%  Similarity=0.418  Sum_probs=67.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       428 l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      |||+|||+++|+++|+++|++||.|..++++.++.++.++|||||+|.+.++|.+|++.||     |..|.|+.|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~ln-----g~~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALK-----ASGVQAQMA   70 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHH-----HHTCCEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhC-----CCEECCEEC
Confidence            7999999999999999999999999999999998899999999999999999999999999     999999876

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.6e-15  Score=122.97  Aligned_cols=79  Identities=16%  Similarity=0.262  Sum_probs=70.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee-CCeeEEEEE
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF-GKRPIAVDW  292 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~-~g~~i~v~~  292 (676)
                      ++.++|||+|||.++++++|+++|+.||.|..+.+...    +++|||||+|.+.++|.+|+..|+|..+ .|+.|+|.|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            45679999999999999999999999999988877653    3678999999999999999999999988 589999999


Q ss_pred             ecCC
Q 005812          293 AVPK  296 (676)
Q Consensus       293 a~~~  296 (676)
                      +++.
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            8753

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=8.4e-16  Score=128.73  Aligned_cols=80  Identities=21%  Similarity=0.221  Sum_probs=72.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      ..+|||+|||+.+|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|+. +|     +..|+||.|.|
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n-----~~~i~gr~i~V   81 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LH-----RKKLNGREAFV   81 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GC-----SEEETTEEEEE
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cC-----CCeECCcEEEE
Confidence            4689999999999999999999999998875566666789999999999999999999995 89     99999999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      .++..+
T Consensus        82 ~~~~~~   87 (103)
T d2cpya1          82 HVVTLE   87 (103)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            997544

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=9.7e-16  Score=125.06  Aligned_cols=80  Identities=25%  Similarity=0.449  Sum_probs=72.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHH----hhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEE
Q 005812          215 QKWKLIIRNIPFKAKVNEIKD----MFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAV  290 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~----~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v  290 (676)
                      ++++|||+|||+.+++++|++    +|++||.|.+|.+..   ++.++|||||+|.+.++|..|++.|||..+.|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            457999999999999998864    689999999998865   4668899999999999999999999999999999999


Q ss_pred             EEecCCC
Q 005812          291 DWAVPKN  297 (676)
Q Consensus       291 ~~a~~~~  297 (676)
                      .|++++.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9997754

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=2.3e-15  Score=122.01  Aligned_cols=82  Identities=22%  Similarity=0.271  Sum_probs=71.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          421 EDELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      +..|+++|||+|||+++++++|+++|++||.|.++++..+      ++||||+|.+.++|.+|+..++..   +..++||
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~---~~~~~g~   74 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAV---TPHLRNQ   74 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHS---CCEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccC---CCccCCC
Confidence            4557899999999999999999999999999999987643      689999999999999999876411   7899999


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      +|.|.|+..+.
T Consensus        75 ~l~v~~sk~~~   85 (88)
T d2cq1a1          75 PIYIQYSNHKE   85 (88)
T ss_dssp             ECEEEECSCSS
T ss_pred             EEEEEECCCCC
Confidence            99999987653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.58  E-value=2.4e-15  Score=117.58  Aligned_cols=74  Identities=20%  Similarity=0.293  Sum_probs=68.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ++|||+|||+++++++|+++|+.||.|..|+++.++..  .++||||+|.++++|++|+. +++..|+|+.|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            48999999999999999999999999999999988643  45799999999999999996 7999999999999864

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=3.6e-15  Score=123.10  Aligned_cols=76  Identities=22%  Similarity=0.461  Sum_probs=68.8

Q ss_pred             CCCCcEEEEcCCC-CCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          213 KTQKWKLIIRNIP-FKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       213 ~~~~~~v~V~nLp-~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....+|||+||| ..+++++|+++|++||.|.+|.|        ++|||||+|.+.++|.+|++.|||..|.|+.|+|+
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   83 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN   83 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3445789999997 57889999999999999999998        35899999999999999999999999999999999


Q ss_pred             EecCC
Q 005812          292 WAVPK  296 (676)
Q Consensus       292 ~a~~~  296 (676)
                      |+.++
T Consensus        84 ~a~~~   88 (98)
T d1wf2a_          84 LAAEP   88 (98)
T ss_dssp             ETTSC
T ss_pred             ECCCC
Confidence            99654

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.58  E-value=2.1e-15  Score=124.43  Aligned_cols=81  Identities=23%  Similarity=0.420  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      .....++|||+|||+++++++|+++|+.||.|..+..     ++.++|||||+|.+.++|.+|++.|||..|.|+.|+|.
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~   86 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3445789999999999999999999999998876543     56699999999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.++.
T Consensus        87 ~a~~k~   92 (96)
T d1fjca_          87 YTGEKG   92 (96)
T ss_dssp             ECSSSC
T ss_pred             EeCCCC
Confidence            998765

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=2.6e-15  Score=123.97  Aligned_cols=74  Identities=27%  Similarity=0.485  Sum_probs=67.7

Q ss_pred             CCCeEEEcCCC-CCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEE
Q 005812          424 LQNTIFICNLP-FDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQL  502 (676)
Q Consensus       424 ~~~~l~V~nLp-~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l  502 (676)
                      .+++|||+||| ..+++++|+++|++||.|..+.|        ++|||||+|.+.++|.+|+..||     |..|+|++|
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~ln-----g~~~~g~~l   80 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGED-----GRMIAGQVL   80 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTT-----TCEETTEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcC-----CCEECCEEE
Confidence            35689999996 57889999999999999999987        37999999999999999999999     999999999


Q ss_pred             EEEEccCc
Q 005812          503 TVLKALDK  510 (676)
Q Consensus       503 ~v~~a~~k  510 (676)
                      .|.++.++
T Consensus        81 ~V~~a~~~   88 (98)
T d1wf2a_          81 DINLAAEP   88 (98)
T ss_dssp             EEEETTSC
T ss_pred             EEEECCCC
Confidence            99998754

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.1e-15  Score=127.61  Aligned_cols=82  Identities=16%  Similarity=0.228  Sum_probs=72.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ...+.+|||+|||+++|++||+++|+.|| +..|.++.+. ++.++|||||+|.+.++|++|++ +|     +..|+||.
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~-----~~~i~gR~   83 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KD-----KANMQHRY   83 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TS-----SCCSSSSC
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cC-----CCEECCEE
Confidence            34467999999999999999999999998 4567777764 58899999999999999999985 89     99999999


Q ss_pred             EEEEEccCch
Q 005812          502 LTVLKALDKK  511 (676)
Q Consensus       502 l~v~~a~~k~  511 (676)
                      |.|.++.++.
T Consensus        84 I~V~~s~~~~   93 (102)
T d1weza_          84 VELFLNSTAG   93 (102)
T ss_dssp             CEEEEECCCC
T ss_pred             EEEEEcCCCC
Confidence            9999987653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=8.9e-16  Score=130.73  Aligned_cols=76  Identities=20%  Similarity=0.100  Sum_probs=69.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      +++|||+|||+.+++++|+++|+.||.|..|.|.      .++|||||+|.+.++|.+|+..||     |..|.|++|.|
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~ln-----g~~~~gr~l~v   78 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLA-----YSKFHHVPLYL   78 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHT-----TCBSSSSBCEE
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHc-----CCccCCCeEEE
Confidence            4799999999999999999999999999998763      357999999999999999999999     99999999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .|+....
T Consensus        79 ~~a~~~~   85 (111)
T d1whxa_          79 EWAPIGV   85 (111)
T ss_dssp             EEEETTT
T ss_pred             EECCCCc
Confidence            9987643

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=3.3e-15  Score=120.84  Aligned_cols=76  Identities=21%  Similarity=0.377  Sum_probs=66.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ...+|||+|||+++++++|+++|++|| +..+.+..      ++|||||+|.+.++|++|++.||+..|.|+.|.|+|+.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~------~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR------NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEG------GGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeec------cCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            356899999999999999999999999 33344433      67999999999999999999999999999999999996


Q ss_pred             CCC
Q 005812          295 PKN  297 (676)
Q Consensus       295 ~~~  297 (676)
                      ++.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2.6e-15  Score=127.26  Aligned_cols=77  Identities=25%  Similarity=0.323  Sum_probs=70.8

Q ss_pred             CcEEEEcCCCC-CCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          216 KWKLIIRNIPF-KAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       216 ~~~v~V~nLp~-~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      +++|||+|||+ .+++++|+++|+.||.|.+|.|+++     .+|||||+|.+.++|.+|++.|||..|.|+.|+|.|+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~-----~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT-----TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEec-----ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            57999999965 5999999999999999999999886     47899999999999999999999999999999999986


Q ss_pred             CCC
Q 005812          295 PKN  297 (676)
Q Consensus       295 ~~~  297 (676)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=6e-15  Score=115.25  Aligned_cols=71  Identities=25%  Similarity=0.448  Sum_probs=64.3

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          219 LIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       219 v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      |||+|||+++++++|+++|++|| +..+.+.+      ++|||||+|.+.++|.+|++.|||..+.|++|.|+|+...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~------~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDK------YKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecc------cceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 55555533      7799999999999999999999999999999999999654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=4.5e-15  Score=115.96  Aligned_cols=71  Identities=30%  Similarity=0.368  Sum_probs=64.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEc
Q 005812          428 IFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA  507 (676)
Q Consensus       428 l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a  507 (676)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.++|.+|+..||     |..+.|++|.|+++
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln-----~~~~~g~~l~V~~a   68 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFH-----QSRLRERELSVQLQ   68 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHT-----TEESSSCEEEEEEC
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhC-----CccCCCCEEEEEEe
Confidence            79999999999999999999999 444433      3568999999999999999999999     99999999999998


Q ss_pred             cCc
Q 005812          508 LDK  510 (676)
Q Consensus       508 ~~k  510 (676)
                      .+.
T Consensus        69 ~~d   71 (75)
T d1wi6a1          69 PTD   71 (75)
T ss_dssp             CST
T ss_pred             CCC
Confidence            653

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

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

Probab=99.56  E-value=6.2e-15  Score=123.64  Aligned_cols=82  Identities=23%  Similarity=0.450  Sum_probs=72.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccC-CCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNT-DTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      .+.++|||+|||+++++++|+++|+.|| |..+.++.+. .++.++|||||+|.+.++|++|++ ||+..|.|+.|+|.|
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            3458999999999999999999999999 6677777655 467899999999999999987775 899999999999999


Q ss_pred             ecCCC
Q 005812          293 AVPKN  297 (676)
Q Consensus       293 a~~~~  297 (676)
                      +.++.
T Consensus        91 a~~~~   95 (104)
T d1wi8a_          91 ADQAQ   95 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            97764

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=3.2e-15  Score=120.89  Aligned_cols=74  Identities=23%  Similarity=0.303  Sum_probs=65.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      +++|||+|||++++++||+++|++|| +..+.+      +..+|||||+|.+.++|.+|+..||     +..|+|++|.|
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln-----~~~~~G~~l~V   72 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFH-----QYSFRGKDLIV   72 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHT-----TEEETTEEEEE
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhC-----CCEECCEEEEE
Confidence            46899999999999999999999999 333333      3468999999999999999999999     99999999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      .++.++
T Consensus        73 ~~a~~~   78 (88)
T d1wg1a_          73 QLQPTD   78 (88)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            998654

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=4.4e-15  Score=123.83  Aligned_cols=83  Identities=24%  Similarity=0.334  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      ......+|||+|||+++|+++|+++|..||. ..|.++.+. ++.++|||||+|.+.++|++|++ +|+..|.||.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            3445679999999999999999999999985 467777775 68899999999999999999997 79999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      |+.+..
T Consensus        88 ~s~~~~   93 (102)
T d1weza_          88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             EcCCCC
Confidence            997764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.56  E-value=4.3e-15  Score=122.66  Aligned_cols=78  Identities=21%  Similarity=0.336  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC--c
Q 005812          423 ELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG--R  500 (676)
Q Consensus       423 ~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g--r  500 (676)
                      .+.++|||+|||+++++++|+++|++||.|..+++.++      ++||||+|.+.++|.+|++.||     +..|.|  +
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~-----~~~i~g~~~   83 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMR-----GFPLGGPDR   83 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHT-----TCBCSSSSC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhC-----CCEeCCCce
Confidence            35689999999999999999999999999999987643      6899999999999999999999     999976  5


Q ss_pred             EEEEEEccCch
Q 005812          501 QLTVLKALDKK  511 (676)
Q Consensus       501 ~l~v~~a~~k~  511 (676)
                      +|+|.||++.+
T Consensus        84 ~l~v~~ak~~~   94 (97)
T d1whya_          84 RLRVDFAKSGP   94 (97)
T ss_dssp             BCEEEECCCCC
T ss_pred             EEEEEeCCCCC
Confidence            89999988653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=2.2e-15  Score=127.79  Aligned_cols=76  Identities=16%  Similarity=0.291  Sum_probs=69.7

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEE
Q 005812          425 QNTIFICNLPF-DLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLT  503 (676)
Q Consensus       425 ~~~l~V~nLp~-~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~  503 (676)
                      +++|||+|||+ .+++++|+++|+.||.|..|.|++++     +|||||+|.++++|.+|++.||     |..|.|+.|.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~ln-----g~~l~g~~l~   71 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLN-----GHKLHGKPIR   71 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHT-----TCBCSSSBCE
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhC-----CCEECCEEEE
Confidence            46999999965 59999999999999999999998763     7899999999999999999999     9999999999


Q ss_pred             EEEccCc
Q 005812          504 VLKALDK  510 (676)
Q Consensus       504 v~~a~~k  510 (676)
                      |.|+..+
T Consensus        72 v~~s~~~   78 (109)
T d2adca1          72 ITLSKHQ   78 (109)
T ss_dssp             EECCSCC
T ss_pred             EEECCCC
Confidence            9998654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.4e-14  Score=117.19  Aligned_cols=80  Identities=20%  Similarity=0.322  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHh--CCceeCCeeEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF--NGQKFGKRPIA  289 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l--~~~~~~g~~i~  289 (676)
                      ...++++|||+|||.++++++|+++|++||.|.++.+.+      .+|||||+|.+.++|.+|++.+  ++..+.|++|+
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~------~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK------GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccc------cceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            345778999999999999999999999999999999886      4589999999999999999865  67789999999


Q ss_pred             EEEecCCC
Q 005812          290 VDWAVPKN  297 (676)
Q Consensus       290 v~~a~~~~  297 (676)
                      |.|++.+.
T Consensus        78 v~~sk~~~   85 (88)
T d2cq1a1          78 IQYSNHKE   85 (88)
T ss_dssp             EEECSCSS
T ss_pred             EEECCCCC
Confidence            99997664

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=2.8e-15  Score=121.39  Aligned_cols=77  Identities=23%  Similarity=0.323  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      ..++|||+|||+.+++++|+++|++||.|.+|+++.+     ++|||||+|.+.++|++|+.  ++..|.|+.|.|.++.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~-----~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec-----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            4679999999999999999999999999999987654     67999999999999999996  7889999999999998


Q ss_pred             CCCC
Q 005812          295 PKNI  298 (676)
Q Consensus       295 ~~~~  298 (676)
                      ++..
T Consensus        77 ~k~~   80 (88)
T d1wf0a_          77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.7e-15  Score=122.62  Aligned_cols=75  Identities=20%  Similarity=0.379  Sum_probs=67.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      +++|||+|||+.+|+++|+++|++||.|..|+++     ..++|||||+|.+.++|++|+.  +     +..|+|++|.|
T Consensus         5 s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~-----~~~i~g~~l~v   72 (88)
T d1wf0a_           5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--E-----DLIIKGISVHI   72 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--C-----EEEETTEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--C-----CCEECCEEeEE
Confidence            5799999999999999999999999999998764     3468999999999999999985  6     78999999999


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .+|.++.
T Consensus        73 ~~a~~k~   79 (88)
T d1wf0a_          73 SNAEPKH   79 (88)
T ss_dssp             ECCCCCC
T ss_pred             EeCCCCC
Confidence            9998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=6e-15  Score=124.48  Aligned_cols=81  Identities=15%  Similarity=0.307  Sum_probs=73.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee--CCeeEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF--GKRPIAV  290 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~--~g~~i~v  290 (676)
                      ..+..+|||+|||+.+|+++|+++|++||.|.+|.++.++    ++|||||+|.+.++|..|+..|||..|  .|+.|.|
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEE
Confidence            3455789999999999999999999999999999998764    689999999999999999999999998  5789999


Q ss_pred             EEecCCC
Q 005812          291 DWAVPKN  297 (676)
Q Consensus       291 ~~a~~~~  297 (676)
                      .|+.++.
T Consensus        80 ~~s~~~~   86 (108)
T d2adba1          80 DFSKLTS   86 (108)
T ss_dssp             EECSSCS
T ss_pred             EecCCcc
Confidence            9987754

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.54  E-value=9.3e-15  Score=120.61  Aligned_cols=79  Identities=18%  Similarity=0.324  Sum_probs=71.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC--eeEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGK--RPIAV  290 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g--~~i~v  290 (676)
                      ..+.++|||+|||+++++++|+++|++||.|..+++.+      .++||||+|.+.++|..|++.||+..|.|  ++|+|
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~------~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v   87 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK------GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS------SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeec------cccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEE
Confidence            34568999999999999999999999999999999976      45899999999999999999999999976  58999


Q ss_pred             EEecCCC
Q 005812          291 DWAVPKN  297 (676)
Q Consensus       291 ~~a~~~~  297 (676)
                      +|+++..
T Consensus        88 ~~ak~~~   94 (97)
T d1whya_          88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EeCCCCC
Confidence            9997643

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=5.4e-15  Score=123.73  Aligned_cols=81  Identities=21%  Similarity=0.234  Sum_probs=72.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          214 TQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ....+|||+|||+++++++|+++|+.||.|..+.++....+|.++|||||+|.+.++|++|++ ||+..|.|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            445789999999999999999999999998875555555689999999999999999999997 8999999999999987


Q ss_pred             cC
Q 005812          294 VP  295 (676)
Q Consensus       294 ~~  295 (676)
                      .+
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            54

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=5.2e-15  Score=124.85  Aligned_cols=78  Identities=18%  Similarity=0.185  Sum_probs=70.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee--cCcEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL--KGRQL  502 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l--~gr~l  502 (676)
                      ..+|||+|||+.+|+++|+++|++||.|..+.++.++    ++|||||+|.++++|.+|+..||     |..|  .|++|
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln-----~~~l~~~~~~l   77 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLD-----GQNIYNACCTL   77 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHH-----SCCSSTTCCCC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHC-----CCEeccCCcEE
Confidence            4689999999999999999999999999999888763    48999999999999999999999     8888  57899


Q ss_pred             EEEEccCch
Q 005812          503 TVLKALDKK  511 (676)
Q Consensus       503 ~v~~a~~k~  511 (676)
                      .|.++.++.
T Consensus        78 ~v~~s~~~~   86 (108)
T d2adba1          78 RIDFSKLTS   86 (108)
T ss_dssp             EEEECSSCS
T ss_pred             EEEecCCcc
Confidence            999987643

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=9.9e-16  Score=123.80  Aligned_cols=73  Identities=19%  Similarity=0.179  Sum_probs=67.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEE
Q 005812          427 TIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLK  506 (676)
Q Consensus       427 ~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~  506 (676)
                      +|||+|||+.+++++|+++|++||.|.++.++.       .|||||+|.+.++|.+|+..||     |..|.|+.|.|.+
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~-----g~~~~g~~i~v~~   69 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLD-----NTKFRSHEGETAY   69 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHT-----TCBCCCTTSCCCB
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhC-----CCEECCcEeEEeE
Confidence            699999999999999999999999999998753       3899999999999999999999     9999999999988


Q ss_pred             ccCch
Q 005812          507 ALDKK  511 (676)
Q Consensus       507 a~~k~  511 (676)
                      +..+.
T Consensus        70 ~~~~~   74 (87)
T d3begb1          70 IRVKV   74 (87)
T ss_dssp             CEEEE
T ss_pred             EecCc
Confidence            76543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=2e-15  Score=121.99  Aligned_cols=73  Identities=21%  Similarity=0.328  Sum_probs=67.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEecCC
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAVPK  296 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~  296 (676)
                      ++|||+|||+++++++|+++|+.||.|.++.+.++       |||||+|.+.++|+.||..|||..|.|+.|.|.++.++
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            36999999999999999999999999999998764       89999999999999999999999999999999887544

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=1e-14  Score=120.31  Aligned_cols=79  Identities=18%  Similarity=0.357  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      ......+|||+|||+.+++++|+++|+.||.|..+.|.+       +|||||+|.+.++|++||+.|||..|.|+.|.|.
T Consensus        11 ~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~   83 (98)
T d1wg4a_          11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETS   83 (98)
T ss_dssp             CCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            445667899999999999999999999999999999864       3899999999999999999999999999999999


Q ss_pred             EecCCC
Q 005812          292 WAVPKN  297 (676)
Q Consensus       292 ~a~~~~  297 (676)
                      ++.++.
T Consensus        84 ~~~~~~   89 (98)
T d1wg4a_          84 YIRVYP   89 (98)
T ss_dssp             EEEEEC
T ss_pred             EEecCC
Confidence            986543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=1.1e-14  Score=121.72  Aligned_cols=80  Identities=13%  Similarity=0.250  Sum_probs=70.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE
Q 005812          422 DELQNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ  501 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~  501 (676)
                      ..++++|||+|||..+++++|+++|++||.|..+++.+      .+|+|||+|.+.++|.+|+..++..   +..++|++
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~------~k~~AfV~f~~~e~A~~ai~~~~~~---~~~~~g~~   82 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFENIDSAKECVTFAADV---PVYIAGQQ   82 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHS---CCBSSSSB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe------cceeEEEEeCCHHHHHHHHHHHcCC---CcEEeeEE
Confidence            34578999999999999999999999999999998763      3789999999999999999987411   67889999


Q ss_pred             EEEEEccCc
Q 005812          502 LTVLKALDK  510 (676)
Q Consensus       502 l~v~~a~~k  510 (676)
                      |.|.|+..+
T Consensus        83 l~v~~s~~~   91 (104)
T d1wexa_          83 AFFNYSTSK   91 (104)
T ss_dssp             CEEEECSSS
T ss_pred             EEEEEcCCC
Confidence            999998764

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=9e-15  Score=120.63  Aligned_cols=74  Identities=12%  Similarity=0.123  Sum_probs=68.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEE
Q 005812          425 QNTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTV  504 (676)
Q Consensus       425 ~~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v  504 (676)
                      ..+|||+|||+.+++++|+++|+.||.|.++.+.       ++|||||+|.+.++|.+|++.||     +..|.|+.|.|
T Consensus        15 ~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~-------~~g~afV~f~~~~~a~~Ai~~ln-----g~~~~g~~i~v   82 (98)
T d1wg4a_          15 DFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ-------KDGMGMVEYLRKEDMEYALRKLD-----DTKFRSHEGET   82 (98)
T ss_dssp             SCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE-------TTTEEEEEESSHHHHHHHHHHHS-----SEEEECTTSCE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhhccccccccc-------ccceEEEEECCHHHHHHHHHHhC-----CCEeCCeEEEE
Confidence            4789999999999999999999999999999874       35899999999999999999999     99999999999


Q ss_pred             EEccCc
Q 005812          505 LKALDK  510 (676)
Q Consensus       505 ~~a~~k  510 (676)
                      .++..+
T Consensus        83 ~~~~~~   88 (98)
T d1wg4a_          83 SYIRVY   88 (98)
T ss_dssp             EEEEEE
T ss_pred             EEEecC
Confidence            998654

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=9.2e-15  Score=120.91  Aligned_cols=78  Identities=24%  Similarity=0.419  Sum_probs=69.4

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH--HcCCCCCCCeeec
Q 005812          422 DELQNTIFICNLPFD-LDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVS--ASKTTSGLGIFLK  498 (676)
Q Consensus       422 ~~~~~~l~V~nLp~~-~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~--~l~~~~~~g~~l~  498 (676)
                      ..++++|||+|||.+ +|+++|.++|++||.|..+.++++      +|+|||+|.+.++|.+|++  .++     +..|+
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~-----~~~~~   83 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKK-----ALWFQ   83 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHS-----CCCSS
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcC-----CceEC
Confidence            345789999999985 899999999999999999988644      6899999999999999998  466     88999


Q ss_pred             CcEEEEEEccCc
Q 005812          499 GRQLTVLKALDK  510 (676)
Q Consensus       499 gr~l~v~~a~~k  510 (676)
                      |++|.|.+|..+
T Consensus        84 gr~l~V~~s~~~   95 (99)
T d1x4fa1          84 GRCVKVDLSEKY   95 (99)
T ss_dssp             SSCCEEEEECSC
T ss_pred             CEEEEEEEcCCc
Confidence            999999998765

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=1e-14  Score=118.00  Aligned_cols=81  Identities=20%  Similarity=0.207  Sum_probs=70.2

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          421 EDELQNTIFICNLPFD-LDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       421 ~~~~~~~l~V~nLp~~-~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      ...++++|||+|||.. +|++||.++|++||.|..+.++.+      +++|||+|.+.++|..|++.|+..   +..++|
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~---~~~~~g   74 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTT---PALVFG   74 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHS---CCEETT
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhC---CCccCC
Confidence            4456789999999986 789999999999999999988754      568999999999999999976311   789999


Q ss_pred             cEEEEEEccCc
Q 005812          500 RQLTVLKALDK  510 (676)
Q Consensus       500 r~l~v~~a~~k  510 (676)
                      ++|.|.||.+.
T Consensus        75 r~l~V~~s~~~   85 (89)
T d1x4da1          75 KPVRVHLSQKY   85 (89)
T ss_dssp             EECEEEEECCC
T ss_pred             ceEEEEECCCc
Confidence            99999998754

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=5.4e-14  Score=117.55  Aligned_cols=81  Identities=12%  Similarity=0.104  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHh--CCceeCCeeEE
Q 005812          212 SKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF--NGQKFGKRPIA  289 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l--~~~~~~g~~i~  289 (676)
                      ...+.++|||+|||..+++++|+++|++||.|..+.+.+      .+|+|||+|.+.++|+.|+..|  ++..+.|++|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~------~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe------cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            345678999999999999999999999999999999976      4689999999999999999977  56678999999


Q ss_pred             EEEecCCCC
Q 005812          290 VDWAVPKNI  298 (676)
Q Consensus       290 v~~a~~~~~  298 (676)
                      |.|+..+..
T Consensus        85 v~~s~~~~~   93 (104)
T d1wexa_          85 FNYSTSKRI   93 (104)
T ss_dssp             EEECSSSSC
T ss_pred             EEEcCCCcc
Confidence            999976543

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=7e-15  Score=124.80  Aligned_cols=83  Identities=23%  Similarity=0.343  Sum_probs=74.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEE
Q 005812          213 KTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDW  292 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~  292 (676)
                      .....+|||+|||+++|+++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|++|++ |||..|+|+.|.|.+
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            4456799999999999999999999999998776666666789999999999999999999997 899999999999998


Q ss_pred             ecCC
Q 005812          293 AVPK  296 (676)
Q Consensus       293 a~~~  296 (676)
                      +.+.
T Consensus        94 ~~~~   97 (112)
T d1wela1          94 ITKK   97 (112)
T ss_dssp             ECHH
T ss_pred             cChH
Confidence            8654

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.50  E-value=4.5e-14  Score=114.09  Aligned_cols=79  Identities=15%  Similarity=0.225  Sum_probs=70.5

Q ss_pred             CCCCCcEEEEcCCCCC-CCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHh--CCceeCCeeE
Q 005812          212 SKTQKWKLIIRNIPFK-AKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKF--NGQKFGKRPI  288 (676)
Q Consensus       212 ~~~~~~~v~V~nLp~~-~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l--~~~~~~g~~i  288 (676)
                      .....++|||+|||.. +|++||+++|++||.|.+|.++.+      +++|||+|.+.++|..|++.|  ++..+.|++|
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            4556789999999986 889999999999999999999874      468999999999999999965  6788999999


Q ss_pred             EEEEecCC
Q 005812          289 AVDWAVPK  296 (676)
Q Consensus       289 ~v~~a~~~  296 (676)
                      +|.|+.+.
T Consensus        78 ~V~~s~~~   85 (89)
T d1x4da1          78 RVHLSQKY   85 (89)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCc
Confidence            99999754

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.49  E-value=4.8e-14  Score=116.52  Aligned_cols=79  Identities=18%  Similarity=0.239  Sum_probs=70.3

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHH--HhCCceeCCeeEE
Q 005812          213 KTQKWKLIIRNIPFK-AKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQ--KFNGQKFGKRPIA  289 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~-~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~--~l~~~~~~g~~i~  289 (676)
                      ...+++|||+|||.. +|+++|+++|++||.|.++.+++      .+|||||+|.+.++|..|++  .+++..|.|+.|+
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~------~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEee------cCCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            345689999999985 89999999999999999999986      45899999999999999997  4688899999999


Q ss_pred             EEEecCCC
Q 005812          290 VDWAVPKN  297 (676)
Q Consensus       290 v~~a~~~~  297 (676)
                      |.|+..+.
T Consensus        89 V~~s~~~~   96 (99)
T d1x4fa1          89 VDLSEKYK   96 (99)
T ss_dssp             EEEECSCS
T ss_pred             EEEcCCcc
Confidence            99996553

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.42  E-value=6.2e-14  Score=116.61  Aligned_cols=76  Identities=12%  Similarity=0.126  Sum_probs=68.1

Q ss_pred             CCeEEEcCCCCCC-C----HHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecC
Q 005812          425 QNTIFICNLPFDL-D----NEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKG  499 (676)
Q Consensus       425 ~~~l~V~nLp~~~-t----eedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~g  499 (676)
                      +++|||+||+.++ +    +++|+++|+.||.|..+.+++      +++||||+|.+.++|.+|+..||     |..|+|
T Consensus         5 ~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~ln-----g~~~~g   73 (104)
T d1weya_           5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLH-----KTEFLG   73 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTST-----TSEETT
T ss_pred             CceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhc-----ccccCC
Confidence            4799999999886 3    367999999999999998863      47899999999999999999999     999999


Q ss_pred             cEEEEEEccCch
Q 005812          500 RQLTVLKALDKK  511 (676)
Q Consensus       500 r~l~v~~a~~k~  511 (676)
                      ++|.|.||+++.
T Consensus        74 ~~l~v~~a~~~~   85 (104)
T d1weya_          74 KEMKLYFAQTLH   85 (104)
T ss_dssp             EECEEECCCCSS
T ss_pred             CEeEEeecccCC
Confidence            999999997653

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=1.1e-13  Score=115.05  Aligned_cols=79  Identities=13%  Similarity=0.044  Sum_probs=70.3

Q ss_pred             CCCcEEEEcCCCCCC-C----HHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeE
Q 005812          214 TQKWKLIIRNIPFKA-K----VNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPI  288 (676)
Q Consensus       214 ~~~~~v~V~nLp~~~-~----e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i  288 (676)
                      ....+|||+||+..+ +    .++|+.+|+.||.|.++.+.+      +++||||+|.+.++|.+|++.|||..|.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            356789999999876 3    367999999999999999986      56899999999999999999999999999999


Q ss_pred             EEEEecCCCC
Q 005812          289 AVDWAVPKNI  298 (676)
Q Consensus       289 ~v~~a~~~~~  298 (676)
                      +|.|+.+...
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999977654

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=4.7e-15  Score=120.72  Aligned_cols=75  Identities=25%  Similarity=0.497  Sum_probs=66.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEe-----ecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCc
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPV-----LHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~-----~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      ++|||+|||+.+|+++|+++|+.||.+..+.+.     .+..++.++|||||+|.+.++|.+|+ .||     |..|.|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~-----g~~~~Gr   75 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFD-----GIIFQGQ   75 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGS-----SCCSSSS
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhC-----CcEECCE
Confidence            589999999999999999999999988766443     34456788999999999999999998 599     9999999


Q ss_pred             EEEEEE
Q 005812          501 QLTVLK  506 (676)
Q Consensus       501 ~l~v~~  506 (676)
                      .|.|.+
T Consensus        76 ~l~V~r   81 (90)
T d1u2fa_          76 SLKIRR   81 (90)
T ss_dssp             CCCCBC
T ss_pred             EEEECC
Confidence            999965

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=4e-13  Score=113.75  Aligned_cols=82  Identities=18%  Similarity=0.126  Sum_probs=69.3

Q ss_pred             CCCCeE-EEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCH-HHHHHHHHHcCCCCCCCeeecCc
Q 005812          423 ELQNTI-FICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTV-EAATAAVSASKTTSGLGIFLKGR  500 (676)
Q Consensus       423 ~~~~~l-~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~-~~A~~Al~~l~~~~~~g~~l~gr  500 (676)
                      +.++.| ||+|||+.+|+++|+++|++||+|.+|.|+.+      +|||||+|.++ ++|..|+..|+     +..+.++
T Consensus         8 ~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~-----~~~l~~~   76 (113)
T d1owxa_           8 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDAN-----NGNLQLR   76 (113)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTT-----TSCBCTT
T ss_pred             CCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhc-----CCceecC
Confidence            345555 99999999999999999999999999998743      79999999996 68999999999     8888888


Q ss_pred             EEEEEEccCchhhhh
Q 005812          501 QLTVLKALDKKLAHD  515 (676)
Q Consensus       501 ~l~v~~a~~k~~~~~  515 (676)
                      .+.|.++..+.....
T Consensus        77 ~~~v~~~~~~~~~e~   91 (113)
T d1owxa_          77 NKEVTWEVLEGEVEK   91 (113)
T ss_dssp             SSSEEEEECCHHHHH
T ss_pred             ceEEEEeeccchhhH
Confidence            888888776654443

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=8.1e-14  Score=115.90  Aligned_cols=76  Identities=21%  Similarity=0.207  Sum_probs=71.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEe
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWA  293 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a  293 (676)
                      ..++|++++..+++++|+++|++||.|.+|.|+++ .++.++|||||+|.+.++|.+|++.|||..|.|+.|.|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            35778888889999999999999999999999877 48899999999999999999999999999999999999986

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=8.4e-14  Score=115.81  Aligned_cols=76  Identities=16%  Similarity=0.179  Sum_probs=71.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVL  505 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~  505 (676)
                      ..++|++++..+++++|+++|++||.|.+|+|+.+ .++.++|+|||+|.+.++|.+|+..||     |..|+||+|.|.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~ln-----g~~~~gr~i~v~  101 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLN-----NRWFNGQPIHAE  101 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHT-----TCEETTEECCEE
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHC-----CCEECCEEEEEE
Confidence            46889999999999999999999999999998766 578999999999999999999999999     999999999999


Q ss_pred             Ec
Q 005812          506 KA  507 (676)
Q Consensus       506 ~a  507 (676)
                      ++
T Consensus       102 ~s  103 (104)
T d1jmta_         102 LS  103 (104)
T ss_dssp             EC
T ss_pred             EC
Confidence            85

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=8.7e-15  Score=119.11  Aligned_cols=76  Identities=21%  Similarity=0.386  Sum_probs=67.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcc-----cCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEE
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPH-----NTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVD  291 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~-----~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~  291 (676)
                      ++|||+|||+++++++|+++|+.||.|..+.+..     +..++.++|||||+|.+.++|+.|++ |||..+.|+.|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            5899999999999999999999999887766543     33567789999999999999999996 99999999999997


Q ss_pred             Ee
Q 005812          292 WA  293 (676)
Q Consensus       292 ~a  293 (676)
                      .+
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            53

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=2.2e-12  Score=106.21  Aligned_cols=85  Identities=22%  Similarity=0.348  Sum_probs=72.5

Q ss_pred             CCCCCCcEEEEcCC--CCCCC---------HHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhC
Q 005812          211 GSKTQKWKLIIRNI--PFKAK---------VNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN  279 (676)
Q Consensus       211 ~~~~~~~~v~V~nL--p~~~~---------e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  279 (676)
                      ......++|+|+||  |.++.         +++|++.|++||.|..|.+..+.    .+|||||+|.+.++|.+|+..||
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~----~~G~~fV~f~~~e~A~~A~~~ln   78 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLD   78 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC----TTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC----CccEEEEEECCHHHHHHHHHHhC
Confidence            34566789999999  55431         36899999999999999987753    67999999999999999999999


Q ss_pred             CceeCCeeEEEEEecCCCCC
Q 005812          280 GQKFGKRPIAVDWAVPKNIY  299 (676)
Q Consensus       280 ~~~~~g~~i~v~~a~~~~~~  299 (676)
                      |..|.|+.|.|.++.++..+
T Consensus        79 g~~~~gr~i~v~~~~g~~~~   98 (99)
T d2dita1          79 GRWFGGRQITAQAWDGTTDY   98 (99)
T ss_dssp             TCEETTEECEEEECCSCCCS
T ss_pred             CcEECCEEEEEEEeCCcCCC
Confidence            99999999999998776543

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=2.3e-12  Score=106.39  Aligned_cols=65  Identities=15%  Similarity=0.213  Sum_probs=57.8

Q ss_pred             CCCCCeEEEcC--CCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeee
Q 005812          422 DELQNTIFICN--LPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFL  497 (676)
Q Consensus       422 ~~~~~~l~V~n--Lp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l  497 (676)
                      ..++++|+|.|  ||..+|+++|+++|++||.|..++++.+      ++||||+|.+.++|.+|+..||     |..+
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~ln-----g~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLN-----GKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTT-----TCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhC-----CCCC
Confidence            34567899966  9999999999999999999999977543      6799999999999999999999     8877

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.28  E-value=3.6e-12  Score=104.83  Aligned_cols=79  Identities=23%  Similarity=0.415  Sum_probs=68.3

Q ss_pred             CCCeEEEcCC--CCCC---------CHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCC
Q 005812          424 LQNTIFICNL--PFDL---------DNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSG  492 (676)
Q Consensus       424 ~~~~l~V~nL--p~~~---------teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~  492 (676)
                      .+++|+|+||  |.++         .++||++.|++||.|..|.+..+    .++|+|||+|.++++|.+|+..||    
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~ln----   78 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLD----   78 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHST----
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhC----
Confidence            4589999999  6543         24789999999999999987644    468999999999999999999999    


Q ss_pred             CCeeecCcEEEEEEccCch
Q 005812          493 LGIFLKGRQLTVLKALDKK  511 (676)
Q Consensus       493 ~g~~l~gr~l~v~~a~~k~  511 (676)
                       |..|+||+|.|.++.++.
T Consensus        79 -g~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          79 -GRWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             -TCEETTEECEEEECCSCC
T ss_pred             -CcEECCEEEEEEEeCCcC
Confidence             999999999999987653

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=3.6e-12  Score=107.74  Aligned_cols=75  Identities=15%  Similarity=0.149  Sum_probs=66.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCH-HHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          216 KWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCK-RDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       216 ~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~-~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      -..+||+|||+.+|+++|+.+|++||.|.+|.|++      .+|||||.|.++ ++|..|+..|++..+.++.+.|.|..
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~------~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR------GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT------TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEec------CCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            34569999999999999999999999999999986      469999999985 78999999999999988888888775


Q ss_pred             CC
Q 005812          295 PK  296 (676)
Q Consensus       295 ~~  296 (676)
                      ..
T Consensus        85 ~~   86 (113)
T d1owxa_          85 LE   86 (113)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=4.7e-12  Score=104.52  Aligned_cols=66  Identities=20%  Similarity=0.394  Sum_probs=59.2

Q ss_pred             CCCCCcEEEEcC--CCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 005812          212 SKTQKWKLIIRN--IPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF  283 (676)
Q Consensus       212 ~~~~~~~v~V~n--Lp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  283 (676)
                      ...+..+++|.|  ||.++|+++|+++|++||.|..|.++.+      ++||||+|.+.++|..|++.|||..+
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            345567888855  9999999999999999999999998873      57999999999999999999999987

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.20  E-value=9.9e-12  Score=97.61  Aligned_cols=74  Identities=16%  Similarity=0.275  Sum_probs=63.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCee-EEEEEe
Q 005812          215 QKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRP-IAVDWA  293 (676)
Q Consensus       215 ~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~-i~v~~a  293 (676)
                      +.+.|+|.|+|++.+++.| ++|++||.|.++++.+      .+|||||+|.++++|++||+ +||..|.|+. |.|...
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            3568999999999986554 6899999999998865      56899999999999999997 8999999974 678876


Q ss_pred             cCC
Q 005812          294 VPK  296 (676)
Q Consensus       294 ~~~  296 (676)
                      ..+
T Consensus        75 ~~k   77 (81)
T d1wwha1          75 IDK   77 (81)
T ss_dssp             CCH
T ss_pred             CCh
Confidence            543

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.20  E-value=1.7e-11  Score=96.25  Aligned_cols=73  Identities=15%  Similarity=0.263  Sum_probs=62.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcE-EEE
Q 005812          426 NTIFICNLPFDLDNEEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQ-LTV  504 (676)
Q Consensus       426 ~~l~V~nLp~~~teedl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~-l~v  504 (676)
                      +.|+|.++|++.+++ +..+|++||.|.++++.      +.+|||||+|.++++|.+||+ +|     |..|+|+. |.|
T Consensus         5 ~wV~V~G~p~~~~~~-il~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~n-----G~~~~g~~~vgV   71 (81)
T d1wwha1           5 TWVTVFGFPQASASY-ILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KD-----GRIFGESIMIGV   71 (81)
T ss_dssp             GEEEEECCCGGGHHH-HHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TT-----TCEETTTEECEE
T ss_pred             cEEEEECCChHHHHH-HHHHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cC-----CCeECCcEEEEE
Confidence            689999999998865 55689999999999763      457999999999999999995 89     99999986 569


Q ss_pred             EEccCch
Q 005812          505 LKALDKK  511 (676)
Q Consensus       505 ~~a~~k~  511 (676)
                      .++..+.
T Consensus        72 ~~~~~k~   78 (81)
T d1wwha1          72 KPCIDKN   78 (81)
T ss_dssp             EECCCHH
T ss_pred             EeCCChh
Confidence            8887654

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=7.4e-12  Score=104.09  Aligned_cols=82  Identities=20%  Similarity=0.175  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCC--CCCC--------CHHHHHHHHHhCCceeEEEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHcCCC
Q 005812          423 ELQNTIFICNL--PFDL--------DNEEVKQRFSAFGEVVSFVPVLHQVT--KRPKGTGFLKFKTVEAATAAVSASKTT  490 (676)
Q Consensus       423 ~~~~~l~V~nL--p~~~--------teedl~~~F~~~G~v~~v~i~~~~~~--~~~~g~afV~F~t~~~A~~Al~~l~~~  490 (676)
                      +|+++|.|+||  |..+        ..+||++.|++||.|.+|.|+++...  ....|++||+|.+.++|.+|+..||  
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~--   79 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLT--   79 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHS--
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHC--
Confidence            35689999999  5554        24689999999999999998876543  3356899999999999999999999  


Q ss_pred             CCCCeeecCcEEEEEEccC
Q 005812          491 SGLGIFLKGRQLTVLKALD  509 (676)
Q Consensus       491 ~~~g~~l~gr~l~v~~a~~  509 (676)
                         |..++||+|.+.++..
T Consensus        80 ---Gr~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          80 ---GRKFANRVVVTKYCDP   95 (104)
T ss_dssp             ---SCCSSSSCCEEEEECH
T ss_pred             ---CCEECCeEEEEEEcCH
Confidence               9999999999999764

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.12  E-value=3.5e-11  Score=99.88  Aligned_cols=82  Identities=30%  Similarity=0.447  Sum_probs=69.8

Q ss_pred             CCCcEEEEcCC--CCCCC--------HHHHHHhhccCCceEEEEEcccCCC--CCceeEEEEEecCHHHHHHHHHHhCCc
Q 005812          214 TQKWKLIIRNI--PFKAK--------VNEIKDMFSPVGLVWNVYIPHNTDT--GLSKGFAFVKFTCKRDAESAIQKFNGQ  281 (676)
Q Consensus       214 ~~~~~v~V~nL--p~~~~--------e~~l~~~F~~~G~i~~v~i~~~~~~--~~~~g~afV~f~~~~~A~~A~~~l~~~  281 (676)
                      .++++|.|+|+  |..+.        .++|++.|++||.|.+|.|++++.+  ....|++||+|.+.++|.+|++.|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            35678999999  55432        4679999999999999999886544  345689999999999999999999999


Q ss_pred             eeCCeeEEEEEecC
Q 005812          282 KFGKRPIAVDWAVP  295 (676)
Q Consensus       282 ~~~g~~i~v~~a~~  295 (676)
                      .++||.|.|.++.+
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999854

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.30  E-value=0.0004  Score=53.73  Aligned_cols=84  Identities=13%  Similarity=0.107  Sum_probs=67.8

Q ss_pred             CeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHHHcCC
Q 005812          578 TRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRVLNNN  657 (676)
Q Consensus       578 ~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~lng~  657 (676)
                      ++|.||+||..+||+++.+.+.         +.|.+........+.+    .....-..|+|.|.+.++...-.+.++|+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~---------~~~~~d~~~f~~Gk~s----~~~~~~SRAYi~F~~~~~v~~F~~~f~g~   68 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQ---------PMPEHDYFEFFSNDTS----LYPHMYARAYINFKNQEDIILFRDRFDGY   68 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHC---------SCCCEEEEEEEESCCS----STTCCCEEEEEEESSSHHHHHHHHHHTTC
T ss_pred             ceEEEecCCCCCCHHHHHHHhC---------CcCceEEEEEeCCCcC----CCCCcceEEEEEeCCHHHHHHHHHHcCCc
Confidence            6899999999999999999997         5788887766655432    23444589999999999999999999998


Q ss_pred             CC--CCCcccCcccccccc
Q 005812          658 PS--KLFYHHCFDAADAQC  674 (676)
Q Consensus       658 ~~--~~~~~~~~~~~~~~~  674 (676)
                      ..  .-|-..+++|.+|..
T Consensus        69 ~F~D~~g~~~~a~VE~AP~   87 (91)
T d1uw4a_          69 VFLDNKGQEYPAIVEFAPF   87 (91)
T ss_dssp             EEECTTCCEEECEEEECSS
T ss_pred             EEEcCCCCEeeeEEEEcCc
Confidence            65  445666888888875

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.18  E-value=0.00085  Score=51.84  Aligned_cols=78  Identities=19%  Similarity=0.252  Sum_probs=62.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCC--ceeEEEEEecCHHHHHHHHHHhCCceeC---C--eeEE
Q 005812          217 WKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGL--SKGFAFVKFTCKRDAESAIQKFNGQKFG---K--RPIA  289 (676)
Q Consensus       217 ~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~--~~g~afV~f~~~~~A~~A~~~l~~~~~~---g--~~i~  289 (676)
                      ++|.|+.||+++|++++.+.++..|.+........+.+.+  .-.-|||.|.+.++.....+.++|..|.   |  ..-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            4799999999999999999999999988776665443322  2346999999999999999999999883   2  2446


Q ss_pred             EEEec
Q 005812          290 VDWAV  294 (676)
Q Consensus       290 v~~a~  294 (676)
                      |++|.
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            77773

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.07  E-value=0.0013  Score=47.22  Aligned_cols=60  Identities=17%  Similarity=0.221  Sum_probs=51.6

Q ss_pred             HHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEc
Q 005812          440 EEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA  507 (676)
Q Consensus       440 edl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a  507 (676)
                      +-|.+.|+++|.|.++.|.... .+  .-.|-|...+..+|.-|+..|+     ...|++++|.|.++
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg--~~~A~V~v~~~q~A~~~v~~Lh-----R~KiG~KRI~Vs~~   70 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DY--QLKAVVQMENLQDAIGAVNSLH-----RYKIGSKKILVSLA   70 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-ST--TCCEEEEESSHHHHHHHHHHHT-----TEEETTEEEEEEEC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CC--cEEEEEEcCCHHHHHHHHHHHH-----HHhcCCeEEEEEEe
Confidence            4556789999999999887653 23  4468999999999999999999     99999999999986

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.61  E-value=0.0015  Score=49.47  Aligned_cols=72  Identities=15%  Similarity=0.195  Sum_probs=57.6

Q ss_pred             CCCCcEEEEcCCCCCCC---------HHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 005812          213 KTQKWKLIIRNIPFKAK---------VNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKF  283 (676)
Q Consensus       213 ~~~~~~v~V~nLp~~~~---------e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  283 (676)
                      .++..+|.|.=......         -.+|.+.|..||.|.-|+++.+.        .+|+|.+-..|-+|+. ++|..+
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d~--------mwVTF~dG~SAL~al~-l~g~~v   82 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCCe--------EEEEECCcHHHHHHhc-cCCeEE
Confidence            34556777765543332         24678889999999999998763        8999999999999999 699999


Q ss_pred             CCeeEEEEEe
Q 005812          284 GKRPIAVDWA  293 (676)
Q Consensus       284 ~g~~i~v~~a  293 (676)
                      +|+.|.|..-
T Consensus        83 ~G~~l~It~~   92 (95)
T d1ufwa_          83 KGRAVKISGP   92 (95)
T ss_dssp             TTEEEEEECC
T ss_pred             cceEEEEecC
Confidence            9999999753

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.58  E-value=0.0039  Score=44.67  Aligned_cols=61  Identities=25%  Similarity=0.278  Sum_probs=51.8

Q ss_pred             HHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeeEEEEEec
Q 005812          231 NEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFNGQKFGKRPIAVDWAV  294 (676)
Q Consensus       231 ~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~  294 (676)
                      +-|.+.|.++|.|.++.+.... +|  .-.|-|...+..+|..|+..|+...|++++|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-ST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CC--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            4456789999999999997643 33  2459999999999999999999999999999999874

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.32  E-value=0.0056  Score=46.19  Aligned_cols=54  Identities=19%  Similarity=0.316  Sum_probs=46.9

Q ss_pred             HHHHHHHHhCCceeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCCCCCeeecCcEEEEEEc
Q 005812          440 EEVKQRFSAFGEVVSFVPVLHQVTKRPKGTGFLKFKTVEAATAAVSASKTTSGLGIFLKGRQLTVLKA  507 (676)
Q Consensus       440 edl~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~F~t~~~A~~Al~~l~~~~~~g~~l~gr~l~v~~a  507 (676)
                      .+|.+.|..||.|.-|+++-+        ...|+|.+-+.|.+|+ .++     +.++.|+.|.|...
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al-~l~-----g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVL-DVD-----GMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHH-HGG-----GSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHh-ccC-----CeEEcceEEEEecC
Confidence            477889999999999988754        4799999999999998 578     99999999999763

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.85  E-value=0.042  Score=42.07  Aligned_cols=61  Identities=16%  Similarity=0.253  Sum_probs=49.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHhhccCCceEEEEEcccCCCCCceeEEEEEecCHHHHHHHHHHhC
Q 005812          211 GSKTQKWKLIIRNIPFKAKVNEIKDMFSPVGLVWNVYIPHNTDTGLSKGFAFVKFTCKRDAESAIQKFN  279 (676)
Q Consensus       211 ~~~~~~~~v~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  279 (676)
                      .......-||.-.+|..+...||.++|++||.|. |..+-+  +     -|||...+.++|+.++..+.
T Consensus        10 d~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd--T-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          10 DLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD--T-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET--T-----EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC--c-----eEEEEecCHHHHHHHHHHhc
Confidence            3455566788889999999999999999999987 444433  1     39999999999999998643

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.83  E-value=0.12  Score=39.49  Aligned_cols=61  Identities=18%  Similarity=0.295  Sum_probs=50.8

Q ss_pred             cccCCeEEEecCCcccCHHHHHHHHHHHHHhhhcccCCCceEeeeeeccccCCCCCCCCcceEEEEEeCChHHHHHHHHH
Q 005812          574 HVSRTRLVIYNLPKSMTEKGLKKLCIDAVVSRASKQKPVIKQIKFLQSLKKGKVDTKHYSRGVAFVEFTEHQHALVALRV  653 (676)
Q Consensus       574 ~~~~~~l~V~nlp~~~te~~l~~~F~~~~~~~~~~~~G~V~~v~i~~~~~~~~~~~~~~s~g~afV~F~~~~~A~~Ai~~  653 (676)
                      ...+.-||.-..|..+...||.++|+         +||.|. |-.+-+             -.|||.....++|..++..
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFS---------pfG~V~-VswIdd-------------TSa~V~L~~~e~~~~v~~~   68 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFS---------AFGNIQ-ISWIDD-------------TSAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHT---------TTCSCC-CEEEET-------------TEEEEECSCHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhc---------CCCceE-EEEecC-------------ceEEEEecCHHHHHHHHHH
Confidence            33556799999999999999999999         799886 666633             3899999999999999988


Q ss_pred             HcCC
Q 005812          654 LNNN  657 (676)
Q Consensus       654 lng~  657 (676)
                      ++-+
T Consensus        69 ~~~~   72 (100)
T d1whva_          69 SKYA   72 (100)
T ss_dssp             HHHC
T ss_pred             hccC
Confidence            7743