Psyllid ID: psy15852

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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-
Protein Sequence
MTAESQDVEMTTTENGQENGGAPVSVKDDDRKLFCPLSSYLELDYLQLWQYFDWVSSSFSENCLLEDSIGKPLTVSCSHHYYLFDQILRTHFFYIMEAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFYSN
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccEEEcccccccccHHHHHHHHHccccEEEEEEEcccccccccccccccEEEEccEEEccccccccccccccEEEccccccccHHHHHHHHccccEEEEEEEcccccccccccEEEEEccHHHHHHHHHHHHHcccccEEccccccccccccccccEEEEcccccccHHHHHHHHHccccEEEEEEEccccccccccEEEEEEcccHHHHHHHHcccEEEccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccEEEEccccccccccccccEEEcccccccEEEEcccccccccccccccccccEEEEEcccccHHHHHHcccccEEEEEEEccccccccccEEEEEEcccHHHHHHHHcccEEEccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccHHHHHHHHHccccEEEEEEEEcccccccccEEEEEEcccHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEEcccccccEEEEEccccccccccccccccccccccccEEEEcccccccHHHHHHHHHHcccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHcccccccccEEEcEEEccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEEccccccccccEEEEEccHHHHHHHHHccccEEcccEEEEEEcccccccccHcccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccccccHHHHHHHHcHHHHHHHcccccccHHHcccHHHHHHccHHHcccccccccccccEEEEcccccccccEEEEEEcccEEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHccccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccHccccccEEEEccccEEccccccccEEEEHHHHHHHcccccccccccHHHHHHHHHHcccEEEEEEEEcccccccccEEEEEEcccccccHEEEccccEEcc
Coil and Loop (DISEMBL)
mtaesqdvemtttengqenggapvsvkdddrklfcplssyleLDYLQLWQYFDwvsssfsenclledsigkpltvscshHYYLFDQILRTHFFYIMEAKnkmvshpgiVHKITEELKEHFskygeienvtlksdpntgrsrgfAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAkaksgkifvgglspemkDEEIKAHFAQFGNiietempydksksqrknfcfiTFEHESVVIDLlknpkqkindkevdvkkatpkpepfgvrggrggrggrggrggrmaggyggyggygggyggilykplLFYELNElgisgrslvcrtgpmvqatpplaevdVTGVIMILLGaknhnsdenptsrshpsqnAIKLYLTRSsyrewghvadnlllcdnfpsireleipeafltktttvpmtttEHMVLVTGTDMMHMEVTEAVPMEiietempydksksqrknfcfiTFEHESVVIDLlknpkqkindkevdvkkatpkpepfgvrggrggrggrggrggrmaggyggyggygggygelDYLQLWQFFDwisssfsenclledsigkpltvscshyhylfdqNLRTHYFYIVEAKnkmvshpgiVDKITEELKEHFSkygeienvtlksdpntgrsrgfAFIVFKDteslekasvedvyfysn
Flexible Loop (DISEMBL)
mtaesqdvemtttengqenggapvsvkdddRKLFCPLSSYLELDYLQLWQYFDWVSSSFSENCLLEDSIGKPLTVSCSHHYYLFDQILRTHFFYIMEAKNKMVSHPGIVHKITEELKEHFSKYGEIEnvtlksdpntgrsRGFAFIVFKDTESLEKASVEdviaegnhvinnkkieakkakaksgkifvgglspeMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVidllknpkqkindkevdvkkatpkpepfgvrggrggrggrggrggRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKnhnsdenptsrshpsqnAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIpeafltktttvpmttTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVidllknpkqkindkevdvkkatpkpepfgvrggrggrggrggrggrMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYgeienvtlksdpntgrsRGFAFIVfkdteslekasvedvyfysn
Low Complexity Region (SEG)
MTAESQDVEMTTTENGQENGGAPVSVKDDDRKLFCPLSSYLELDYLQLWQYFDWVSSSFSENCLLEDSIGKPLTVSCSHHYYLFDQILRTHFFYIMEAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNkkieakkakaksgkIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEPFgvrggrggrggrggrggrmaggyggyggygggyggILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLtktttvpmtttEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEPFgvrggrggrggrggrggrmaggyggyggygggygELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFYSN
Disordered region (IsUnstruct)
*******************************KLFCPLSSYLELDYLQLWQYFDWVSSSFSENCLLEDSIGKPLTVSCSHHYYLFDQILRTHFFYIMEAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTL********SRGFAFIVFKDTESLEKASVEDVIAEGNHVINN*************KIFVGGL********IKAHFAQFGNIIETEMPY******RKNFCFITFEHESVVIDLLK*****************************************MAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGA******************AIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETE*********RKNFCFITFEHESVVIDLLK*****************************************MAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTL********SRGFAFIVFKDTESLEKASVEDVYF***
Disordered Region (DISOPRED)
********************************LFCPLSSYLELDYLQLWQYFDWVSSSFSENCLLEDSIGKPLTVSCSHHYYLF******************VSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVIN***IE*****AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDV*********************************************************************************************************************YLTRSSYREWGHVADNLLLCDNFPSIREL**********************LVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDV**********************GGRGGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDS*********************************MVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF***
Disordered Region (DISEMBL)
*********************APVSVKDDDRKLFCPLSSYLELDYLQLWQYFDWVSSSFSENCLLEDSIGKPLTVSCSHHYYLFDQILRTHFFYIMEAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE********GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEPFGVRGG**********GGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKNH*************QNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEPFGVRGG**********GGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFYSN
Disordered Region (DISPRO)
*****************************DRKLFCPLSSYLELDYLQLWQYFDWVSSSFSENCLLEDSIGKPLTVSCSHHYYLFDQIL*********AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP****************RGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKN************PSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK******************RGGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFYSN
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTAESQDVEMTTTENGQENGGAPVSVKDDDRKLFCPLSSYLELDYLQLWQYFDWVSSSFSENCLLEDSIGKPLTVSCSHHYYLFDQILRTHFFYIMEAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFYSN
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	661	2.2.26 [Sep-21-2011]
Q08473	344	RNA-binding protein squid	no	N/A	0.232	0.447	0.65	4e-54
Q3SWU3	322	Heterogeneous nuclear rib	no	N/A	0.219	0.450	0.419	7e-28
Q5ZI72	301	Heterogeneous nuclear rib	yes	N/A	0.219	0.481	0.425	8e-28
O14979	420	Heterogeneous nuclear rib	no	N/A	0.219	0.345	0.419	1e-27
Q6NU14	291	Heterogeneous nuclear rib	N/A	N/A	0.219	0.498	0.412	2e-27
Q9Z130	301	Heterogeneous nuclear rib	no	N/A	0.219	0.481	0.419	3e-27
Q640A2	297	Heterogeneous nuclear rib	no	N/A	0.219	0.488	0.412	3e-27
Q7ZX83	293	Heterogeneous nuclear rib	N/A	N/A	0.219	0.494	0.412	4e-27
Q99020	285	Heterogeneous nuclear rib	no	N/A	0.219	0.508	0.422	2e-26
Q60668	355	Heterogeneous nuclear rib	no	N/A	0.219	0.408	0.406	8e-26

>sp|Q08473|SQD_DROME RNA-binding protein squid OS=Drosophila melanogaster GN=sqd PE=1 SV=3

 Score =  213 bits (542), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 104/160 (65%), Positives = 128/160 (80%), Gaps = 6/160 (3%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + TE EL++HF KYGEIE++ +K+DP TGRSRGFAFIVF +TE+++K S  D    
Sbjct: 62  GLSWETTEKELRDHFGKYGEIESINVKTDPQTGRSRGFAFIVFTNTEAIDKVSAAD---- 117

Query: 166 GNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQR 225
             H+IN+KK++ KKAKA+ GKIFVGGL+ E+ DEEIK +F QFGNI+E EMP+DK KSQR
Sbjct: 118 -EHIINSKKVDPKKAKARHGKIFVGGLTTEISDEEIKTYFGQFGNIVEVEMPFDKQKSQR 176

Query: 226 KNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           K FCFITF+ E VV DLLK PKQKI  KEVDVK+ATPKPE
Sbjct: 177 KGFCFITFDSEQVVTDLLKTPKQKIAGKEVDVKRATPKPE 216

This protein is a component of ribonucleosomes. Could be needed to organize a concentration gradient of a dorsalizing morphogen (Dm) originating in the germinal vesicle. At least one of the isoforms is essential in somatic tissues.
Drosophila melanogaster (taxid: 7227)

>sp|Q3SWU3|HNRDL_RAT Heterogeneous nuclear ribonucleoprotein D-like OS=Rattus norvegicus GN=Hnrpdl PE=2 SV=1

 Score =  125 bits (315), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 65/155 (41%), Positives = 98/155 (63%), Gaps = 10/155 (6%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           ++L E+ S++GE+ + T+K+DP TGRSRGF F++FKD      ASV+ V+    H ++ K
Sbjct: 65  KDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDA-----ASVDKVLELKEHKLDGK 119

Query: 174 KIEAKKAKAKSGK-----IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF 228
            I+ K+AKA  GK     +FVGGLSP+  +E+IK +F  FG I   E+P D   ++R+ F
Sbjct: 120 LIDPKRAKALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGF 179

Query: 229 CFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           CFIT+  E  V  LL++   +I   + ++K A PK
Sbjct: 180 CFITYTDEEPVKKLLESRYHQIGSGKCEIKVAQPK 214

Acts as a transcriptional regulator. Promotes transcription repression. Promotes transcription activation in differentiated myotubes. Binds to double- and single-stranded DNA sequences. Binds to the transcription suppressor CATR sequence of the COX5B promoter. Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto-oncogenes and cytokine mRNAs. Binds both to nuclear and cytoplasmic poly(A) mRNAs. Binds to poly(G) and poly(A), but not to poly(U) or poly(C) RNA homopolymers. Binds to the 5'-ACUAGC-3' RNA consensus sequence.

Rattus norvegicus (taxid: 10116)

>sp|Q5ZI72|HNRDL_CHICK Heterogeneous nuclear ribonucleoprotein D-like OS=Gallus gallus GN=HNRPDL PE=2 SV=1

 Score =  125 bits (315), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 66/155 (42%), Positives = 98/155 (63%), Gaps = 10/155 (6%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           ++L E+ S++GE+ + T+K+DP TGRSRGF F++FKD      ASVE V+    H ++ K
Sbjct: 44  KDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDA-----ASVEKVLELKEHKLDGK 98

Query: 174 KIEAKKAKAKSGK-----IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF 228
            I+ K+AKA  GK     +FVGGLSP+  +E+IK +F  FG I   E+P D   ++R+ F
Sbjct: 99  LIDPKRAKALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGF 158

Query: 229 CFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           CFIT+  E  V  LL++   +I   + ++K A PK
Sbjct: 159 CFITYTDEEPVKKLLESRYHQIGSGKCEIKVAQPK 193

Acts as a transcriptional regulator. Binds DNA and RNA.

Gallus gallus (taxid: 9031)

>sp|O14979|HNRDL_HUMAN Heterogeneous nuclear ribonucleoprotein D-like OS=Homo sapiens GN=HNRPDL PE=1 SV=3

 Score =  125 bits (313), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 65/155 (41%), Positives = 98/155 (63%), Gaps = 10/155 (6%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           ++L E+ S++GE+ + T+K+DP TGRSRGF F++FKD      ASV+ V+    H ++ K
Sbjct: 162 KDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDA-----ASVDKVLELKEHKLDGK 216

Query: 174 KIEAKKAKAKSGK-----IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF 228
            I+ K+AKA  GK     +FVGGLSP+  +E+IK +F  FG I   E+P D   ++R+ F
Sbjct: 217 LIDPKRAKALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGF 276

Query: 229 CFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           CFIT+  E  V  LL++   +I   + ++K A PK
Sbjct: 277 CFITYTDEEPVKKLLESRYHQIGSGKCEIKVAQPK 311

Acts as a transcriptional regulator. Promotes transcription repression. Promotes transcription activation in differentiated myotubes (By similarity). Binds to double- and single-stranded DNA sequences. Binds to the transcription suppressor CATR sequence of the COX5B promoter (By similarity). Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto-oncogenes and cytokine mRNAs. Binds both to nuclear and cytoplasmic poly(A) mRNAs. Binds to poly(G) and poly(A), but not to poly(U) or poly(C) RNA homopolymers. Binds to the 5'-ACUAGC-3' RNA consensus sequence.

Homo sapiens (taxid: 9606)

>sp|Q6NU14|HNDLB_XENLA Heterogeneous nuclear ribonucleoprotein D-like-B OS=Xenopus laevis GN=hnrpdl-b PE=2 SV=1

 Score =  125 bits (313), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 64/155 (41%), Positives = 97/155 (62%), Gaps = 10/155 (6%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           ++L E+ S++GE+ + T+K+DP TGRSRGF F++FKD       SV+ V+    H ++ K
Sbjct: 48  KDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDA-----VSVDKVLETKEHKLDGK 102

Query: 174 KIEAKKAKAKSGK-----IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF 228
            I+ K+AKA  GK     +FVGGLSPE  +E+IK +F  FG I   E+P D   ++R+ F
Sbjct: 103 LIDPKRAKALQGKEPPKKVFVGGLSPETTEEQIKQYFGGFGEIENIELPMDTKTNERRGF 162

Query: 229 CFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           CF+T+  E  V  LL++   +I   + ++K A PK
Sbjct: 163 CFVTYTDEEPVQKLLESRFHQIGTGKCEIKAAQPK 197

Acts as a transcriptional regulator. Binds DNA and RNA.

Xenopus laevis (taxid: 8355)

>sp|Q9Z130|HNRDL_MOUSE Heterogeneous nuclear ribonucleoprotein D-like OS=Mus musculus GN=Hnrpdl PE=1 SV=1

 Score =  124 bits (310), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 65/155 (41%), Positives = 98/155 (63%), Gaps = 10/155 (6%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           ++L E+ S++GE+ + T+K+DP TGRSRGF F++FKD      ASV+ V+    H ++ K
Sbjct: 43  KDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDA-----ASVDKVLELKEHKLDGK 97

Query: 174 KIEAKKAKAKSGK-----IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF 228
            I+ K+AKA  GK     +FVGGLSP+  +E+IK +F  FG I   E+P D   ++R+ F
Sbjct: 98  LIDPKRAKALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGF 157

Query: 229 CFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           CFIT+  E  V  LL++   +I   + ++K A PK
Sbjct: 158 CFITYTDEEPVKKLLESRYHQIGSGKCEIKVAQPK 192

Acts as a transcriptional regulator. Promotes transcription repression (By similarity). Promotes transcription activation in differentiated myotubes. Binds to double- and single-stranded DNA sequences (By similarity). Binds to the transcription suppressor CATR sequence of the COX5B promoter. Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto-oncogenes and cytokine mRNAs (By similarity). Binds both to nuclear and cytoplasmic poly(A) mRNAs (By similarity). Binds to poly(G) and poly(A), but not to poly(U) or poly(C) RNA homopolymers (By similarity). Binds to the 5'-ACUAGC-3' RNA consensus sequence.

Mus musculus (taxid: 10090)

>sp|Q640A2|HNRDL_XENTR Heterogeneous nuclear ribonucleoprotein D-like OS=Xenopus tropicalis GN=hnrpdl PE=2 SV=1

 Score =  124 bits (310), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 64/155 (41%), Positives = 97/155 (62%), Gaps = 10/155 (6%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           ++L E+ S++GE+ + T+K+DP TGRSRGF F++FKD       SV+ V+    H ++ K
Sbjct: 40  KDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDA-----VSVDKVLETKEHKLDGK 94

Query: 174 KIEAKKAKAKSGK-----IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF 228
            I+ K+AKA  GK     +FVGGLSPE  +E+IK +F  FG I   E+P D   ++R+ F
Sbjct: 95  LIDPKRAKALKGKEPPKKVFVGGLSPETTEEQIKQYFGGFGEIENIELPMDTKTNERRGF 154

Query: 229 CFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           CF+T+  E  V  LL++   +I   + ++K A PK
Sbjct: 155 CFVTYTGEEPVKKLLESRFHQIGTGKCEIKVAQPK 189

Acts as a transcriptional regulator. Binds DNA and RNA.

Xenopus tropicalis (taxid: 8364)

>sp|Q7ZX83|HNDLA_XENLA Heterogeneous nuclear ribonucleoprotein D-like-A OS=Xenopus laevis GN=hnrpdl-a PE=2 SV=1

 Score =  123 bits (309), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 64/155 (41%), Positives = 97/155 (62%), Gaps = 10/155 (6%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           ++L E+ S++GE+ + T+K+DP TGRSRGF F++FKD       SV+ V+    H ++ K
Sbjct: 40  KDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDA-----VSVDKVLETNEHKLDGK 94

Query: 174 KIEAKKAKAKSGK-----IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF 228
            I+ K+AKA  GK     +FVGGLSPE  +E+IK +F  FG I   E+P D   ++R+ F
Sbjct: 95  LIDPKRAKALKGKEPPKKVFVGGLSPETTEEQIKQYFGGFGEIENIELPIDTKTNERRGF 154

Query: 229 CFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           CF+T+  E  V  LL++   +I   + ++K A PK
Sbjct: 155 CFVTYTGEEPVKKLLESRFHQIGTGKCEIKAAQPK 189

Acts as a transcriptional regulator. Binds DNA and RNA.

Xenopus laevis (taxid: 8355)

>sp|Q99020|ROAA_MOUSE Heterogeneous nuclear ribonucleoprotein A/B OS=Mus musculus GN=Hnrnpab PE=1 SV=1

 Score =  121 bits (304), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 65/154 (42%), Positives = 100/154 (64%), Gaps = 9/154 (5%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           ++LK++F+K+GE+ + T+K DPNTGRSRGF FI+FKD+ S+EK     V+ +  H ++ +
Sbjct: 89  KDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDSSSVEK-----VLDQKEHRLDGR 143

Query: 174 KIEAKKAKAKSG----KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFC 229
            I+ KKA A       KIFVGGL+PE  +E+I+ +F QFG I   E+P D   ++R+ F 
Sbjct: 144 VIDPKKAMAMKKDPVKKIFVGGLNPEATEEKIREYFGQFGEIEAIELPIDPKLNKRRGFV 203

Query: 230 FITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           FITF+ E  V  +L+     ++  + ++K A PK
Sbjct: 204 FITFKEEDPVKKVLEKKFHTVSGSKCEIKVAQPK 237

Transcriptional repressor. Binds to CArG box motifs, single-stranded and double-stranded DNA, and RNA. It may be that repression by CBF-A is a result of competitive binding of CBF, a putative positive factor, and CBF-A to the same or overlapping motifs around the CArG boxes.

Mus musculus (taxid: 10090)

>sp|Q60668|HNRPD_MOUSE Heterogeneous nuclear ribonucleoprotein D0 OS=Mus musculus GN=Hnrnpd PE=1 SV=2

 Score =  119 bits (298), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 63/155 (40%), Positives = 99/155 (63%), Gaps = 10/155 (6%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           ++LK++FSK+GE+ + TLK DP TGRSRGF F++FK++ES++K     V+ +  H +N K
Sbjct: 111 KDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDK-----VMDQKEHKLNGK 165

Query: 174 KIEAKKAKAKS-----GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF 228
            I+ K+AKA        KIFVGGLSP+  +E+I+ +F  FG +   E+P D   ++R+ F
Sbjct: 166 VIDPKRAKAMKTKEPVKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGF 225

Query: 229 CFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           CFITF+ E  V  +++     +   + ++K A  K
Sbjct: 226 CFITFKEEEPVKKIMEKKYHNVGLSKCEIKVAMSK 260

Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto-oncogenes and cytokine mRNAs. Also binds to double- and single-stranded DNA sequences in a specific manner and functions a transcription factor. Each of the RNA-binding domains specifically can bind solely to a single-stranded non-monotonous 5'-UUAG-3' sequence and also weaker to the single-stranded 5'-TTAGGG-3' telomeric DNA repeat. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats. Binding of RRM1 to DNA inhibits the formation of DNA quadruplex structure which may play a role in telomere elongation. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain.

Mus musculus (taxid: 10090)

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	661
1209409	297	hnRNP protein [Chironomus tentans]	0.232	0.518	0.631	9e-53
312372973	293	hypothetical protein AND_19410 [Anophele	0.226	0.511	0.664	1e-52
24646609	321	squid, isoform A [Drosophila melanogaste	0.232	0.479	0.65	2e-52
390178414	310	GA14206, isoform C [Drosophila pseudoobs	0.232	0.496	0.643	2e-52
390178412	319	GA14206, isoform B [Drosophila pseudoobs	0.232	0.482	0.643	2e-52
24646605	308	squid, isoform C [Drosophila melanogaste	0.232	0.5	0.65	2e-52
11040	345	hrp40.2 [Drosophila melanogaster]	0.232	0.446	0.65	3e-52
24646607	344	squid, isoform B [Drosophila melanogaste	0.232	0.447	0.65	3e-52
194901408	345	GG17035 [Drosophila erecta] gi|190651947	0.232	0.446	0.65	3e-52
157110306	292	heterogeneous nuclear ribonucleoprotein	0.222	0.503	0.671	3e-52

>gi|1209409|emb|CAA90716.1| hnRNP protein [Chironomus tentans]

 Score =  214 bits (546), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 101/160 (63%), Positives = 134/160 (83%), Gaps = 6/160 (3%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + TE EL++HF +YGEI+++ +K+DP TGRSRGFAFIV+K  +S++K     V+A 
Sbjct: 46  GLSWETTEKELRDHFGQYGEIDSINVKTDPTTGRSRGFAFIVYKSADSIDK-----VVAA 100

Query: 166 GNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQR 225
           G+H+INNKK++ KKAKA++GKIFVGGL PE+ D+EI+A+FAQFGNI+E EMP+DK K+QR
Sbjct: 101 GDHIINNKKVDPKKAKARTGKIFVGGLIPEISDDEIRAYFAQFGNIVEMEMPFDKQKNQR 160

Query: 226 KNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           K FCFITF+ E+VV +LLK PKQ I+ KEVDVKKATPKP+
Sbjct: 161 KAFCFITFDSETVVNELLKTPKQTISGKEVDVKKATPKPD 200

Source: Chironomus tentans

Species: Chironomus tentans

Genus: Chironomus

Family: Chironomidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312372973|gb|EFR20814.1| hypothetical protein AND_19410 [Anopheles darlingi]

 Score =  214 bits (544), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 103/155 (66%), Positives = 129/155 (83%), Gaps = 5/155 (3%)

Query: 111 KITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVI 170
           +I ++LKEHFS YG+IE++ +K+DPNTGRSRGFAFIV+K+ +S+EK     V+A G+HVI
Sbjct: 104 QIYQDLKEHFSAYGDIESINVKTDPNTGRSRGFAFIVYKNADSIEK-----VVAAGDHVI 158

Query: 171 NNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCF 230
           NNKK++ KKAKA+ GKIFVGGL+ E+ DEEIK  F QFGNI+E EMP+DK K+QRK FCF
Sbjct: 159 NNKKVDPKKAKARHGKIFVGGLTSEISDEEIKIFFGQFGNIVEVEMPFDKQKNQRKGFCF 218

Query: 231 ITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           ITF+ E VV +LLK PKQ I+ KEVDVKKATPKP+
Sbjct: 219 ITFDSEQVVNELLKTPKQTISGKEVDVKKATPKPD 253

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24646609|ref|NP_731826.1| squid, isoform A [Drosophila melanogaster] gi|11038|emb|CAA44503.1| hrp40.1 [Drosophila melanogaster] gi|21428420|gb|AAM49870.1| LD09691p [Drosophila melanogaster] gi|23171185|gb|AAF54964.2| squid, isoform A [Drosophila melanogaster] gi|220943526|gb|ACL84306.1| sqd-PA [synthetic construct] gi|220953540|gb|ACL89313.1| sqd-PA [synthetic construct]

 Score =  214 bits (544), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 104/160 (65%), Positives = 128/160 (80%), Gaps = 6/160 (3%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + TE EL++HF KYGEIE++ +K+DP TGRSRGFAFIVF +TE+++K S  D    
Sbjct: 62  GLSWETTEKELRDHFGKYGEIESINVKTDPQTGRSRGFAFIVFTNTEAIDKVSAAD---- 117

Query: 166 GNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQR 225
             H+IN+KK++ KKAKA+ GKIFVGGL+ E+ DEEIK +F QFGNI+E EMP+DK KSQR
Sbjct: 118 -EHIINSKKVDPKKAKARHGKIFVGGLTTEISDEEIKTYFGQFGNIVEVEMPFDKQKSQR 176

Query: 226 KNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           K FCFITF+ E VV DLLK PKQKI  KEVDVK+ATPKPE
Sbjct: 177 KGFCFITFDSEQVVTDLLKTPKQKIAGKEVDVKRATPKPE 216

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|390178414|ref|XP_001359012.3| GA14206, isoform C [Drosophila pseudoobscura pseudoobscura] gi|388859439|gb|EAL28155.3| GA14206, isoform C [Drosophila pseudoobscura pseudoobscura]

 Score =  213 bits (543), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 103/160 (64%), Positives = 131/160 (81%), Gaps = 6/160 (3%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + TE EL++HF K+GEIE++ +K+DP TGRSRGFAFIVF +TE+++K S     + 
Sbjct: 61  GLSWETTEKELRDHFGKFGEIESINVKTDPQTGRSRGFAFIVFTNTEAIDKVS-----SA 115

Query: 166 GNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQR 225
           G H+IN+KK++ KKAKA+ GKIFVGGL+ E+ DEEIK +F+QFGNI+E EMP+DK KSQR
Sbjct: 116 GEHIINSKKVDPKKAKARHGKIFVGGLTTEISDEEIKTYFSQFGNIVEVEMPFDKQKSQR 175

Query: 226 KNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           K FCFITF+ E VV DLLK PKQKI+ KEVDVK+ATPKPE
Sbjct: 176 KGFCFITFDSEQVVTDLLKTPKQKISGKEVDVKRATPKPE 215

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|390178412|ref|XP_003736644.1| GA14206, isoform B [Drosophila pseudoobscura pseudoobscura] gi|388859438|gb|EIM52717.1| GA14206, isoform B [Drosophila pseudoobscura pseudoobscura]

 Score =  213 bits (543), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 103/160 (64%), Positives = 131/160 (81%), Gaps = 6/160 (3%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + TE EL++HF K+GEIE++ +K+DP TGRSRGFAFIVF +TE+++K S     + 
Sbjct: 61  GLSWETTEKELRDHFGKFGEIESINVKTDPQTGRSRGFAFIVFTNTEAIDKVS-----SA 115

Query: 166 GNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQR 225
           G H+IN+KK++ KKAKA+ GKIFVGGL+ E+ DEEIK +F+QFGNI+E EMP+DK KSQR
Sbjct: 116 GEHIINSKKVDPKKAKARHGKIFVGGLTTEISDEEIKTYFSQFGNIVEVEMPFDKQKSQR 175

Query: 226 KNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           K FCFITF+ E VV DLLK PKQKI+ KEVDVK+ATPKPE
Sbjct: 176 KGFCFITFDSEQVVTDLLKTPKQKISGKEVDVKRATPKPE 215

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24646605|ref|NP_652209.1| squid, isoform C [Drosophila melanogaster] gi|386765705|ref|NP_001247088.1| squid, isoform E [Drosophila melanogaster] gi|23171183|gb|AAN13570.1| squid, isoform C [Drosophila melanogaster] gi|73853364|gb|AAZ86753.1| LD29474p [Drosophila melanogaster] gi|220951946|gb|ACL88516.1| sqd-PC [synthetic construct] gi|383292688|gb|AFH06406.1| squid, isoform E [Drosophila melanogaster]

 Score =  213 bits (542), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 104/160 (65%), Positives = 128/160 (80%), Gaps = 6/160 (3%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + TE EL++HF KYGEIE++ +K+DP TGRSRGFAFIVF +TE+++K S  D    
Sbjct: 62  GLSWETTEKELRDHFGKYGEIESINVKTDPQTGRSRGFAFIVFTNTEAIDKVSAAD---- 117

Query: 166 GNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQR 225
             H+IN+KK++ KKAKA+ GKIFVGGL+ E+ DEEIK +F QFGNI+E EMP+DK KSQR
Sbjct: 118 -EHIINSKKVDPKKAKARHGKIFVGGLTTEISDEEIKTYFGQFGNIVEVEMPFDKQKSQR 176

Query: 226 KNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           K FCFITF+ E VV DLLK PKQKI  KEVDVK+ATPKPE
Sbjct: 177 KGFCFITFDSEQVVTDLLKTPKQKIAGKEVDVKRATPKPE 216

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|11040|emb|CAA44504.1| hrp40.2 [Drosophila melanogaster]

 Score =  213 bits (542), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 104/160 (65%), Positives = 128/160 (80%), Gaps = 6/160 (3%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + TE EL++HF KYGEIE++ +K+DP TGRSRGFAFIVF +TE+++K S  D    
Sbjct: 62  GLSWETTEKELRDHFGKYGEIESINVKTDPQTGRSRGFAFIVFTNTEAIDKVSAAD---- 117

Query: 166 GNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQR 225
             H+IN+KK++ KKAKA+ GKIFVGGL+ E+ DEEIK +F QFGNI+E EMP+DK KSQR
Sbjct: 118 -EHIINSKKVDPKKAKARHGKIFVGGLTTEISDEEIKTYFGQFGNIVEVEMPFDKQKSQR 176

Query: 226 KNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           K FCFITF+ E VV DLLK PKQKI  KEVDVK+ATPKPE
Sbjct: 177 KGFCFITFDSEQVVTDLLKTPKQKIAGKEVDVKRATPKPE 216

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24646607|ref|NP_731825.1| squid, isoform B [Drosophila melanogaster] gi|55584092|sp|Q08473.3|SQD_DROME RecName: Full=RNA-binding protein squid; AltName: Full=Heterogeneous nuclear ribonucleoprotein 40; Short=HNRNP 40 gi|23171184|gb|AAF54963.2| squid, isoform B [Drosophila melanogaster]

 Score =  213 bits (542), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 104/160 (65%), Positives = 128/160 (80%), Gaps = 6/160 (3%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + TE EL++HF KYGEIE++ +K+DP TGRSRGFAFIVF +TE+++K S  D    
Sbjct: 62  GLSWETTEKELRDHFGKYGEIESINVKTDPQTGRSRGFAFIVFTNTEAIDKVSAAD---- 117

Query: 166 GNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQR 225
             H+IN+KK++ KKAKA+ GKIFVGGL+ E+ DEEIK +F QFGNI+E EMP+DK KSQR
Sbjct: 118 -EHIINSKKVDPKKAKARHGKIFVGGLTTEISDEEIKTYFGQFGNIVEVEMPFDKQKSQR 176

Query: 226 KNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           K FCFITF+ E VV DLLK PKQKI  KEVDVK+ATPKPE
Sbjct: 177 KGFCFITFDSEQVVTDLLKTPKQKIAGKEVDVKRATPKPE 216

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194901408|ref|XP_001980244.1| GG17035 [Drosophila erecta] gi|190651947|gb|EDV49202.1| GG17035 [Drosophila erecta]

 Score =  213 bits (542), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 104/160 (65%), Positives = 128/160 (80%), Gaps = 6/160 (3%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + TE EL++HF KYGEIE++ +K+DP TGRSRGFAFIVF +TE+++K S  D    
Sbjct: 62  GLSWETTEKELRDHFGKYGEIESINVKTDPQTGRSRGFAFIVFTNTEAIDKVSAAD---- 117

Query: 166 GNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQR 225
             H+IN+KK++ KKAKA+ GKIFVGGL+ E+ DEEIK +F QFGNI+E EMP+DK KSQR
Sbjct: 118 -EHIINSKKVDPKKAKARHGKIFVGGLTTEISDEEIKTYFGQFGNIVEVEMPFDKQKSQR 176

Query: 226 KNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           K FCFITF+ E VV DLLK PKQKI  KEVDVK+ATPKPE
Sbjct: 177 KGFCFITFDSEQVVTDLLKTPKQKIAGKEVDVKRATPKPE 216

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157110306|ref|XP_001651044.1| heterogeneous nuclear ribonucleoprotein [Aedes aegypti] gi|108878768|gb|EAT42993.1| AAEL005515-PB [Aedes aegypti]

 Score =  213 bits (541), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 102/152 (67%), Positives = 126/152 (82%), Gaps = 5/152 (3%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           +ELKEHF +YGEIE++ +K+DPNTGRSRGFAFIV+K  +S++K     V+A G+HVINNK
Sbjct: 50  KELKEHFGQYGEIESINVKTDPNTGRSRGFAFIVYKSADSIDK-----VVAAGDHVINNK 104

Query: 174 KIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
           K++ KKAKA+ GKIFVGGL+ E+ DEEIK  F QFGNI+E EMP+DK K+QRK FCFITF
Sbjct: 105 KVDPKKAKARHGKIFVGGLTTEISDEEIKTFFGQFGNIVEVEMPFDKQKNQRKGFCFITF 164

Query: 234 EHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           + E VV +LLK PKQ I+ KEVDVKKATPKP+
Sbjct: 165 DSEQVVNELLKTPKQTISGKEVDVKKATPKPD 196

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	661
FB|FBgn0263396	344	sqd "squid" [Drosophila melano	0.232	0.447	0.593	3.8e-46
MGI|MGI:1330294	285	Hnrnpab "heterogeneous nuclear	0.225	0.522	0.393	2e-24
RGD|69255	298	Hnrnpab "heterogeneous nuclear	0.225	0.5	0.393	2e-24
UNIPROTKB|E9PTS0	331	Hnrnpab "Protein Hnrnpab" [Rat	0.225	0.450	0.393	2e-24
UNIPROTKB|Q9QX80	285	Hnrnpab "Hnrpab protein" [Ratt	0.225	0.522	0.393	2e-24
UNIPROTKB|Q9QX81	332	Hnrnpab "RCG34663, isoform CRA	0.225	0.448	0.393	2e-24
UNIPROTKB|Q3ZC44	285	HNRNPAB "Uncharacterized prote	0.225	0.522	0.393	3.2e-24
UNIPROTKB|F1NCW4	258	HNRNPD "Uncharacterized protei	0.229	0.589	0.361	3.2e-24
UNIPROTKB|Q5ZIH1	257	HNRNPD "Uncharacterized protei	0.229	0.591	0.361	3.2e-24
UNIPROTKB|A5D9H5	306	HNRPD "Heterogeneous nuclear r	0.229	0.496	0.361	4.2e-24

FB|FBgn0263396 sqd "squid" [Drosophila melanogaster (taxid:7227)]

 Score = 484 (175.4 bits), Expect = 3.8e-46, P = 3.8e-46
 Identities = 95/160 (59%), Positives = 116/160 (72%)

Query:   107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
             G+  + TE EL++HF KYGEIE++ +K+DP TGRSRGFAFIVF +TE+++K S  D    
Sbjct:    62 GLSWETTEKELRDHFGKYGEIESINVKTDPQTGRSRGFAFIVFTNTEAIDKVSAAD---- 117

Query:   166 GNHVINNXXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQR 225
               H+IN+              IFVGGL+ E+ DEEIK +F QFGNI+E EMP+DK KSQR
Sbjct:   118 -EHIINSKKVDPKKAKARHGKIFVGGLTTEISDEEIKTYFGQFGNIVEVEMPFDKQKSQR 176

Query:   226 KNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
             K FCFITF+ E VV DLLK PKQKI  KEVDVK+ATPKPE
Sbjct:   177 KGFCFITFDSEQVVTDLLKTPKQKIAGKEVDVKRATPKPE 216

GO:0005634 "nucleus" evidence=IC;IDA;TAS

GO:0005730 "nucleolus" evidence=IDA

GO:0005703 "polytene chromosome puff" evidence=IDA

GO:0008069 "dorsal/ventral axis specification, ovarian follicular epithelium" evidence=IMP

GO:0007297 "ovarian follicle cell migration" evidence=IMP

GO:0048477 "oogenesis" evidence=IMP;TAS

GO:0008298 "intracellular mRNA localization" evidence=NAS;TAS

GO:0017148 "negative regulation of translation" evidence=TAS

GO:0003730 "mRNA 3'-UTR binding" evidence=TAS

GO:0009953 "dorsal/ventral pattern formation" evidence=IMP;TAS

GO:0006405 "RNA export from nucleus" evidence=TAS

GO:0030529 "ribonucleoprotein complex" evidence=ISS;NAS

GO:0003729 "mRNA binding" evidence=ISS;NAS

GO:0035062 "omega speckle" evidence=IDA

GO:0000785 "chromatin" evidence=IDA

GO:0005737 "cytoplasm" evidence=TAS

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=TAS

GO:0006406 "mRNA export from nucleus" evidence=NAS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0019094 "pole plasm mRNA localization" evidence=IMP

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IMP

GO:0030720 "oocyte localization involved in germarium-derived egg chamber formation" evidence=IMP

GO:0016325 "oocyte microtubule cytoskeleton organization" evidence=IMP

GO:0007293 "germarium-derived egg chamber formation" evidence=IMP

GO:0007314 "oocyte anterior/posterior axis specification" evidence=IMP

GO:0045451 "pole plasm oskar mRNA localization" evidence=IEP

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0033119 "negative regulation of RNA splicing" evidence=IMP

MGI|MGI:1330294 Hnrnpab "heterogeneous nuclear ribonucleoprotein A/B" [Mus musculus (taxid:10090)]

 Score = 286 (105.7 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 59/150 (39%), Positives = 90/150 (60%)

Query:   114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNX 173
             ++LK++F+K+GE+ + T+K DPNTGRSRGF FI+FKD+ S+EK   +        VI+  
Sbjct:    89 KDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDSSSVEKVLDQKEHRLDGRVIDPK 148

Query:   174 XXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
                          IFVGGL+PE  +E+I+ +F QFG I   E+P D   ++R+ F FITF
Sbjct:   149 KAMAMKKDPVKK-IFVGGLNPEATEEKIREYFGQFGEIEAIELPIDPKLNKRRGFVFITF 207

Query:   234 EHESVVIDLLKNPKQKINDKEVDVKKATPK 263
             + E  V  +L+     ++  + ++K A PK
Sbjct:   208 KEEDPVKKVLEKKFHTVSGSKCEIKVAQPK 237

GO:0000166 "nucleotide binding" evidence=IEA

GO:0001837 "epithelial to mesenchymal transition" evidence=IDA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=ISO

GO:0003688 "DNA replication origin binding" evidence=ISO

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=ISO

GO:0043565 "sequence-specific DNA binding" evidence=IDA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=ISO

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

RGD|69255 Hnrnpab "heterogeneous nuclear ribonucleoprotein A/B" [Rattus norvegicus (taxid:10116)]

 Score = 286 (105.7 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 59/150 (39%), Positives = 90/150 (60%)

Query:   114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNX 173
             ++LK++F+K+GE+ + T+K DPNTGRSRGF FI+FKD+ S+EK   +        VI+  
Sbjct:   102 KDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDSSSVEKVLDQKEHRLDGRVIDPK 161

Query:   174 XXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
                          IFVGGL+PE  +E+I+ +F QFG I   E+P D   ++R+ F FITF
Sbjct:   162 KAMAMKKDPVKK-IFVGGLNPEATEEKIREYFGQFGEIEAIELPIDPKLNKRRGFVFITF 220

Query:   234 EHESVVIDLLKNPKQKINDKEVDVKKATPK 263
             + E  V  +L+     ++  + ++K A PK
Sbjct:   221 KEEDPVKKVLEKKFHTVSGSKCEIKVAQPK 250

GO:0001837 "epithelial to mesenchymal transition" evidence=ISO

GO:0003677 "DNA binding" evidence=IDA

GO:0003688 "DNA replication origin binding" evidence=IDA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=ISO

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IDA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISO

GO:0043565 "sequence-specific DNA binding" evidence=ISO

UNIPROTKB|E9PTS0 Hnrnpab "Protein Hnrnpab" [Rattus norvegicus (taxid:10116)]

 Score = 286 (105.7 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 59/150 (39%), Positives = 90/150 (60%)

Query:   114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNX 173
             ++LK++F+K+GE+ + T+K DPNTGRSRGF FI+FKD+ S+EK   +        VI+  
Sbjct:    88 KDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDSSSVEKVLDQKEHRLDGRVIDPK 147

Query:   174 XXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
                          IFVGGL+PE  +E+I+ +F QFG I   E+P D   ++R+ F FITF
Sbjct:   148 KAMAMKKDPVKK-IFVGGLNPEATEEKIREYFGQFGEIEAIELPIDPKLNKRRGFVFITF 206

Query:   234 EHESVVIDLLKNPKQKINDKEVDVKKATPK 263
             + E  V  +L+     ++  + ++K A PK
Sbjct:   207 KEEDPVKKVLEKKFHTVSGSKCEIKVAQPK 236

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q9QX80 Hnrnpab "Hnrpab protein" [Rattus norvegicus (taxid:10116)]

 Score = 286 (105.7 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 59/150 (39%), Positives = 90/150 (60%)

Query:   114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNX 173
             ++LK++F+K+GE+ + T+K DPNTGRSRGF FI+FKD+ S+EK   +        VI+  
Sbjct:    89 KDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDSSSVEKVLDQKEHRLDGRVIDPK 148

Query:   174 XXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
                          IFVGGL+PE  +E+I+ +F QFG I   E+P D   ++R+ F FITF
Sbjct:   149 KAMAMKKDPVKK-IFVGGLNPEATEEKIREYFGQFGEIEAIELPIDPKLNKRRGFVFITF 207

Query:   234 EHESVVIDLLKNPKQKINDKEVDVKKATPK 263
             + E  V  +L+     ++  + ++K A PK
Sbjct:   208 KEEDPVKKVLEKKFHTVSGSKCEIKVAQPK 237

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|Q9QX81 Hnrnpab "RCG34663, isoform CRA_a" [Rattus norvegicus (taxid:10116)]

 Score = 286 (105.7 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 59/150 (39%), Positives = 90/150 (60%)

Query:   114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNX 173
             ++LK++F+K+GE+ + T+K DPNTGRSRGF FI+FKD+ S+EK   +        VI+  
Sbjct:    89 KDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDSSSVEKVLDQKEHRLDGRVIDPK 148

Query:   174 XXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
                          IFVGGL+PE  +E+I+ +F QFG I   E+P D   ++R+ F FITF
Sbjct:   149 KAMAMKKDPVKK-IFVGGLNPEATEEKIREYFGQFGEIEAIELPIDPKLNKRRGFVFITF 207

Query:   234 EHESVVIDLLKNPKQKINDKEVDVKKATPK 263
             + E  V  +L+     ++  + ++K A PK
Sbjct:   208 KEEDPVKKVLEKKFHTVSGSKCEIKVAQPK 237

GO:0000166 "nucleotide binding" evidence=IEA

GO:0001837 "epithelial to mesenchymal transition" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0043565 "sequence-specific DNA binding" evidence=ISS

UNIPROTKB|Q3ZC44 HNRNPAB "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 284 (105.0 bits), Expect = 3.2e-24, P = 3.2e-24
 Identities = 59/150 (39%), Positives = 89/150 (59%)

Query:   114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNX 173
             ++LK++F+K+GE+ + T+K DPNTGRSRGF FI+FKD  S+EK   +        VI+  
Sbjct:    84 KDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDATSVEKVLDQKEHRLDGRVIDPK 143

Query:   174 XXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
                          IFVGGL+PE  +E+I+ +F +FG I   E+P D   ++R+ F FITF
Sbjct:   144 KAMAMKKDPVKK-IFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKSNKRRGFVFITF 202

Query:   234 EHESVVIDLLKNPKQKINDKEVDVKKATPK 263
             + E  V  +L+     I+  + ++K A PK
Sbjct:   203 KEEEPVKKVLEKKFHTISGSKCEIKVAQPK 232

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1NCW4 HNRNPD "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 284 (105.0 bits), Expect = 3.2e-24, P = 3.2e-24
 Identities = 55/152 (36%), Positives = 89/152 (58%)

Query:   114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNX 173
             ++LK++FSK+GE+ + TLK DP TGRSRGF F++FK++ES++K   +        VI+  
Sbjct:    14 KDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPK 73

Query:   174 XXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
                          IFVGGLSP+  +E+I+ +F  FG +   E+P D   ++R+ FCFITF
Sbjct:    74 RAKAMKTKEPVKKIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITF 133

Query:   234 EHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
             + E  V  +++     +   + ++K A  K +
Sbjct:   134 KEEEPVKKIMEKKYHNVGLSKCEIKVAMSKEQ 165

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0042162 "telomeric DNA binding" evidence=IEA

GO:0043488 "regulation of mRNA stability" evidence=IEA

UNIPROTKB|Q5ZIH1 HNRNPD "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 284 (105.0 bits), Expect = 3.2e-24, P = 3.2e-24
 Identities = 55/152 (36%), Positives = 89/152 (58%)

Query:   114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNX 173
             ++LK++FSK+GE+ + TLK DP TGRSRGF F++FK++ES++K   +        VI+  
Sbjct:    13 KDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPK 72

Query:   174 XXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
                          IFVGGLSP+  +E+I+ +F  FG +   E+P D   ++R+ FCFITF
Sbjct:    73 RAKAMKTKEPVKKIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITF 132

Query:   234 EHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
             + E  V  +++     +   + ++K A  K +
Sbjct:   133 KEEEPVKKIMEKKYHNVGLSKCEIKVAMSKEQ 164

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0042162 "telomeric DNA binding" evidence=IEA

GO:0043488 "regulation of mRNA stability" evidence=IEA

UNIPROTKB|A5D9H5 HNRPD "Heterogeneous nuclear ribonucleoprotein D" [Bos taurus (taxid:9913)]

 Score = 283 (104.7 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 55/152 (36%), Positives = 89/152 (58%)

Query:   114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNX 173
             ++LK++FSK+GE+ + TLK DP TGRSRGF F++FK++ES++K   +        VI+  
Sbjct:   111 KDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPK 170

Query:   174 XXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
                          IFVGGLSP+  +E+I+ +F  FG +   E+P D   ++R+ FCFITF
Sbjct:   171 RAKAMKTKEPVKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 230

Query:   234 EHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
             + E  V  +++     +   + ++K A  K +
Sbjct:   231 KEEEPVKKIMEKKYHNVGLSKCEIKVAMSKEQ 262

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" 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 EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	661
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	6e-30
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	6e-21
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	8e-18
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	1e-16
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	1e-16
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	6e-16
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-15
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	2e-15
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	4e-15
smart00360	73	smart00360, RRM, RNA recognition motif	7e-15
smart00360	73	smart00360, RRM, RNA recognition motif	1e-14
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	1e-14
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	2e-14
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-14
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	8e-14
smart00360	73	smart00360, RRM, RNA recognition motif	1e-13
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-13
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	2e-13
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-13
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-13
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-13
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	7e-13
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	8e-13
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	8e-13
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-12
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-12
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	2e-12
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	2e-12
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	3e-12
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-12
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	4e-12
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-12
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	6e-12
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	6e-12
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	7e-12
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-12
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	8e-12
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	9e-12
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	9e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	9e-12
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	9e-12
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-11
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-11
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	2e-11
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	3e-11
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-11
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	3e-11
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	3e-11
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	3e-11
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	4e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-11
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	9e-11
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	1e-10
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-10
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	1e-10
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-10
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-10
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-10
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	3e-10
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-10
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	4e-10
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	4e-10
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	5e-10
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	6e-10
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	6e-10
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	7e-10
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	7e-10
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	7e-10
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	8e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	8e-10
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-09
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-09
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-09
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-09
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	3e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-09
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	4e-09
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	4e-09
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	4e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	5e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	5e-09
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	5e-09
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	5e-09
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-09
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	8e-09
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	9e-09
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-08
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-08
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-08
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-08
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-08
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	1e-08
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-08
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-08
cd12724	92	cd12724, RRM1_CPEB2_like, RNA recognition motif 1	4e-08
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	5e-08
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	5e-08
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-08
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	6e-08
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	7e-08
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	7e-08
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	7e-08
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	9e-08
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	9e-08
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	9e-08
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	1e-07
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	1e-07
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	1e-07
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-07
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	1e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-07
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	1e-07
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-07
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	1e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-07
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-07
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-07
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	2e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-07
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	2e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-07
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-07
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-07
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	2e-07
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-07
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	3e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-07
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	3e-07
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	3e-07
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	3e-07
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	4e-07
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-07
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-07
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-07
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	4e-07
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	5e-07
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	5e-07
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	5e-07
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	5e-07
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	6e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	7e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	7e-07
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	8e-07
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	8e-07
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	8e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	8e-07
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	9e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	9e-07
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	1e-06
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	1e-06
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	1e-06
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-06
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	2e-06
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	2e-06
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	2e-06
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	2e-06
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-06
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	2e-06
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	2e-06
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	2e-06
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	2e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	3e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-06
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-06
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	3e-06
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	3e-06
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	3e-06
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	3e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	4e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-06
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	4e-06
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	4e-06
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	5e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	5e-06
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	5e-06
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	5e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	5e-06
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	6e-06
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	6e-06
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	6e-06
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	6e-06
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	6e-06
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	6e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	6e-06
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	7e-06
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	8e-06
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	8e-06
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	8e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	9e-06
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	9e-06
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	9e-06
pfam07172	91	pfam07172, GRP, Glycine rich protein family	9e-06
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	1e-05
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-05
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-05
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	2e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	2e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-05
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	2e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-05
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	2e-05
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	2e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-05
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	2e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-05
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-05
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-05
pfam07172	91	pfam07172, GRP, Glycine rich protein family	3e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	3e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	3e-05
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	3e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-05
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	4e-05
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	4e-05
pfam07172	91	pfam07172, GRP, Glycine rich protein family	4e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	4e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	4e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	4e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-05
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	5e-05
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	5e-05
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	5e-05
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	5e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	5e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	5e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	5e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	6e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	6e-05
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	6e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	6e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	6e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	6e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	6e-05
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	7e-05
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	7e-05
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	8e-05
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	8e-05
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	8e-05
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	8e-05
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	9e-05
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	9e-05
PLN03120	260	PLN03120, PLN03120, nucleic acid binding protein;	9e-05
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	1e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	1e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	1e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	1e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-04
pfam07172	91	pfam07172, GRP, Glycine rich protein family	2e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	2e-04
PLN03120	260	PLN03120, PLN03120, nucleic acid binding protein;	2e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	2e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	2e-04
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	2e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-04
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	2e-04
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	2e-04
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	2e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	2e-04
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	3e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-04
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	3e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-04
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	3e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	3e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	3e-04
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	3e-04
cd12228	84	cd12228, RRM_ENOX, RNA recognition motif (RRM) in	3e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-04
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	4e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	4e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	4e-04
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	4e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	4e-04
PRK06958	182	PRK06958, PRK06958, single-stranded DNA-binding pr	4e-04
cd12302	110	cd12302, RRM_scSet1p_like, RNA recognition motif i	4e-04
cd12302	110	cd12302, RRM_scSet1p_like, RNA recognition motif i	4e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	4e-04
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	4e-04
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	4e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	4e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	4e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	4e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	5e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	5e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	5e-04
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	5e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	6e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	6e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	6e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	6e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	6e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	6e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	7e-04
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	7e-04
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	7e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	7e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	7e-04
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	7e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	7e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	7e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	8e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	8e-04
cd12294	102	cd12294, RRM_Rrp7A, RNA recognition motif in ribos	8e-04
cd12294	102	cd12294, RRM_Rrp7A, RNA recognition motif in ribos	8e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	9e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	9e-04
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	0.001
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	0.001
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.001
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	0.001
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	0.001
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	0.001
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.001
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.001
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.001
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.001
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.001
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	0.001
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	0.001
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.001
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	0.001
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	0.001
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	0.001
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	0.001
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	0.001
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	0.001
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.001
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	0.001
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	0.002
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.002
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	0.002
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	0.002
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	0.002
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	0.002
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.002
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.002
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.002
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	0.002
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	0.002
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	0.002
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.002
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.002
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.002
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	0.002
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.002
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.002
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.002
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	0.002
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	0.003
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.003
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.003
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	0.003
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.003
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	0.003
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.003
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	0.003
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	0.003
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	0.003
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	0.003
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	0.003
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.004
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	0.004
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	0.004
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.004
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	0.004
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	0.004
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.004
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.004
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	0.004
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	0.004

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score =  112 bits (282), Expect = 6e-30
 Identities = 39/75 (52%), Positives = 54/75 (72%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           KIFVGGLSPE  +E+I+ +F +FGNI+E E+P DK  ++R+ FCFITF+ E  V  +L+ 
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

Query: 246 PKQKINDKEVDVKKA 260
               I  K+V+VKKA
Sbjct: 61  QFHVIGGKKVEVKKA 75

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, 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. It 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 memembers 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 = 75

>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 = 86.5 bits (215), Expect = 6e-21
 Identities = 29/66 (43%), Positives = 43/66 (65%), Gaps = 5/66 (7%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
            E L+E+FSKYGE+ +  +  DP TGRSRGF F+ F D      +SV+ V+A   HV++ 
Sbjct: 12  EESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFAD-----PSSVDKVLAAKPHVLDG 66

Query: 173 KKIEAK 178
           ++I+ K
Sbjct: 67  REIDPK 72

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|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 77.8 bits (192), Expect = 8e-18
 Identities = 28/75 (37%), Positives = 48/75 (64%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           KIFVGGL P++ +EE K +F+QFG +++ ++  D    + + F F+TF+ ES V  +   
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 246 PKQKINDKEVDVKKA 260
              ++  K+V+VK+A
Sbjct: 61  GMLELGGKQVEVKRA 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|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 74.7 bits (184), Expect = 1e-16
 Identities = 23/51 (45%), Positives = 33/51 (64%)

Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
            I+E E+P DK  ++R+ FCFITF+ E  V  +L+     I  K+V+VKKA
Sbjct: 25  NIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILETQFHVIGGKKVEVKKA 75

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, 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. It 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 memembers 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 = 75

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 74.7 bits (184), Expect = 1e-16
 Identities = 32/80 (40%), Positives = 50/80 (62%)

Query: 183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDL 242
           ++ KIFVGGL P + + +++ +F+QFG + E  + YD  K + + F FITFE E  V  +
Sbjct: 1   RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

Query: 243 LKNPKQKINDKEVDVKKATP 262
           +      IN K+V+VK+A P
Sbjct: 61  VNEHFHDINGKKVEVKRAEP 80

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 72.5 bits (178), Expect = 6e-16
 Identities = 32/68 (47%), Positives = 44/68 (64%), Gaps = 5/68 (7%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
            E L+E+FSK+GEI+   +  DP T RSRGF F+ F D      ASV+ V+A+G H ++ 
Sbjct: 12  AEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSD-----PASVDKVLAQGPHELDG 66

Query: 173 KKIEAKKA 180
           KKI+ K A
Sbjct: 67  KKIDPKVA 74

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

>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 = 71.8 bits (176), Expect = 1e-15
 Identities = 31/67 (46%), Positives = 48/67 (71%), Gaps = 5/67 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           ++LKE+FSK+GE+ + T+K DP TGRSRGF F++FKD  S+EK     V+ +  H ++ +
Sbjct: 13  KDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEK-----VLDQKEHKLDGR 67

Query: 174 KIEAKKA 180
            I+ K+A
Sbjct: 68  VIDPKRA 74

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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 71.6 bits (175), Expect = 2e-15
 Identities = 32/67 (47%), Positives = 49/67 (73%), Gaps = 5/67 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           ++LK++F+K+GE+ + T+K DPNTGRSRGF FI+FKD  S+EK     V+ +  H ++ +
Sbjct: 14  KDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEK-----VLEQKEHRLDGR 68

Query: 174 KIEAKKA 180
            I+ KKA
Sbjct: 69  LIDPKKA 75

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which 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 A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>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 = 69.9 bits (172), Expect = 4e-15
 Identities = 23/45 (51%), Positives = 31/45 (68%)

Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            E L+E+FSKYGE+ +  +  DP TGRSRGF F+ F D  S++K 
Sbjct: 12  EESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKV 56

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|214636 smart00360, RRM, RNA recognition motif

 Score = 69.5 bits (171), Expect = 7e-15
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            +FVG L P+  +EE++  F++FG +    +  DK   + K F F+ FE E      L+ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 246 -PKQKINDKEVDV 257
              ++++ + + V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 68.8 bits (169), Expect = 1e-14
 Identities = 25/63 (39%), Positives = 40/63 (63%), Gaps = 4/63 (6%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           EEL+E FSK+G++E+V L  D  TG+S+GFAF+ F+  E  EKA    + A     ++ +
Sbjct: 14  EELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKA----LEALNGKELDGR 69

Query: 174 KIE 176
            ++
Sbjct: 70  PLK 72

Length = 73

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 68.9 bits (168), Expect = 1e-14
 Identities = 32/67 (47%), Positives = 50/67 (74%), Gaps = 5/67 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           ++LK++FSK+GE+ + TLK DP TGRSRGF F++FK++ES++K     V+ +  H +N K
Sbjct: 13  KDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDK-----VMDQKEHKLNGK 67

Query: 174 KIEAKKA 180
            I+ K+A
Sbjct: 68  VIDPKRA 74

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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 68.1 bits (166), Expect = 2e-14
 Identities = 30/75 (40%), Positives = 47/75 (62%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+FVGGLSP+  +E+IK +F  FG I   E+P D   ++R+ FCF+T+  E  V  LL++
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

Query: 246 PKQKINDKEVDVKKA 260
              +I   + ++K A
Sbjct: 61  RYHQIGSGKCEIKVA 75

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), 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. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>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 = 67.4 bits (165), Expect = 3e-14
 Identities = 31/75 (41%), Positives = 48/75 (64%), Gaps = 6/75 (8%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+   +TE E KE+FS++G++ +  L  D +TGRSRGF F+ F D+ES    +VE V + 
Sbjct: 6   GLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF-DSES----AVERVFSA 60

Query: 166 GNHVINNKKIEAKKA 180
           G   +  K++E K+A
Sbjct: 61  GMLELGGKQVEVKRA 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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 66.4 bits (162), Expect = 8e-14
 Identities = 27/47 (57%), Positives = 37/47 (78%)

Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           D   ++LKE+FSK+GE+ + T+K DP TGRSRGF F++FKD  S+EK
Sbjct: 9   DTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEK 55

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|214636 smart00360, RRM, RNA recognition motif

 Score = 66.1 bits (162), Expect = 1e-13
 Identities = 24/44 (54%), Positives = 33/44 (75%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           EEL+E FSK+G++E+V L  D  TG+S+GFAF+ F+  E  EKA
Sbjct: 14  EELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKA 57

Length = 73

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 66.2 bits (162), Expect = 1e-13
 Identities = 26/78 (33%), Positives = 46/78 (58%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+F+GGLS E  D+ +K +F+Q+G I +  +  D +  + + F F+TF   S V   +  
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 246 PKQKINDKEVDVKKATPK 263
              K++ +EV+ K+A P+
Sbjct: 61  RPHKVDGREVEPKRAVPR 78

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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 65.4 bits (159), Expect = 2e-13
 Identities = 27/47 (57%), Positives = 38/47 (80%)

Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           D   ++LK++F+K+GE+ + T+K DPNTGRSRGF FI+FKD  S+EK
Sbjct: 10  DTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEK 56

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which 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 A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 65.5 bits (160), Expect = 2e-13
 Identities = 29/74 (39%), Positives = 48/74 (64%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           KIFVGGLS    ++++K +F+QFG + +  + +DK  ++ + F F+TFE E VV  + + 
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 246 PKQKINDKEVDVKK 259
              +IN+K V+ KK
Sbjct: 61  HFHEINNKMVECKK 74

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 65.5 bits (160), Expect = 2e-13
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 7/78 (8%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  K TE +LK++FS +GE+  V +K DP TG+S+GF F+ F D E   K         
Sbjct: 6   GLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV------LS 59

Query: 166 GNHVINNKKIEAKKAKAK 183
             H+I+ +  + K   +K
Sbjct: 60  QRHMIDGRWCDVKIPNSK 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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 63.8 bits (156), Expect = 6e-13
 Identities = 25/63 (39%), Positives = 39/63 (61%), Gaps = 5/63 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           E+LK+ FSK+G IE++ +  D  TGRS+GFAF+ F+D E  EKA    + A     +  +
Sbjct: 13  EDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKA----LEALNGKELGGR 67

Query: 174 KIE 176
           ++ 
Sbjct: 68  ELR 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|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 66.2 bits (161), Expect = 7e-13
 Identities = 37/118 (31%), Positives = 57/118 (48%), Gaps = 8/118 (6%)

Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
           S K+F+GGLS    D  ++  FA FG++++ ++  D+   + + F F+ F  E      +
Sbjct: 34  STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI 93

Query: 244 KNPKQK-INDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGY 300
                K +N + + V  A  +P      GG GG  G G       GGYGG G  GGG+
Sbjct: 94  SEMDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGG-------GGYGGGGDGGGGF 144

Length = 144

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 63.9 bits (156), Expect = 8e-13
 Identities = 28/75 (37%), Positives = 44/75 (58%), Gaps = 6/75 (8%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+   +TE +L+++FS++G +  V +  D    R RGF FI F+  +     SV+ V+ E
Sbjct: 9   GLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESED-----SVDQVVNE 63

Query: 166 GNHVINNKKIEAKKA 180
             H IN KK+E K+A
Sbjct: 64  HFHDINGKKVEVKRA 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|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 63.9 bits (156), Expect = 8e-13
 Identities = 25/78 (32%), Positives = 46/78 (58%), Gaps = 6/78 (7%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+ ++ T++ LK +FS++GEI +  +  DPNT RSRGF F+ F        + V+  +  
Sbjct: 6   GLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFAS-----ASEVDAAMNA 60

Query: 166 GNHVINNKKIEAKKAKAK 183
             H ++ +++E K+A  +
Sbjct: 61  RPHKVDGREVEPKRAVPR 78

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

 Score = 63.4 bits (155), Expect = 1e-12
 Identities = 25/68 (36%), Positives = 41/68 (60%), Gaps = 5/68 (7%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
            + L+++FS++GEIE   + +D  TG+SRG+ F+ FKD ES E+A       + N +I+ 
Sbjct: 14  DDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA-----CKDPNPIIDG 68

Query: 173 KKIEAKKA 180
           +K     A
Sbjct: 69  RKANVNLA 76

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

 Score = 62.2 bits (152), Expect = 2e-12
 Identities = 19/72 (26%), Positives = 41/72 (56%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           +F+GGLS +  +E ++ +F+++G +++  +  D    + + F F+TF   S V  +L   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 247 KQKINDKEVDVK 258
              ++ +E+D K
Sbjct: 61  PHVLDGREIDPK 72

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|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 62.7 bits (152), Expect = 2e-12
 Identities = 29/68 (42%), Positives = 47/68 (69%), Gaps = 5/68 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           ++L E+ S++GE+ + T+K+DP TGRSRGF F++FKD  S++K     V+    H ++ K
Sbjct: 14  KDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDK-----VLELKEHKLDGK 68

Query: 174 KIEAKKAK 181
            I+ K+AK
Sbjct: 69  LIDPKRAK 76

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which 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. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 62.3 bits (151), Expect = 2e-12
 Identities = 28/75 (37%), Positives = 46/75 (61%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           KIFVGGLSP+  +E+I+ +F  FG +   E+P D   ++R+ FCFITF+ E  V  +++ 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 246 PKQKINDKEVDVKKA 260
               +   + ++K A
Sbjct: 61  KYHNVGLSKCEIKVA 75

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, 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 = 75

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

 Score = 62.2 bits (152), Expect = 3e-12
 Identities = 21/45 (46%), Positives = 33/45 (73%)

Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            + L+++FS++GEIE   + +D  TG+SRG+ F+ FKD ES E+A
Sbjct: 14  DDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 68.8 bits (168), Expect = 3e-12
 Identities = 61/260 (23%), Positives = 96/260 (36%), Gaps = 41/260 (15%)

Query: 111 KITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV 169
           K  E +L E FSK G++ +V    D N+ RS+G A++ F D ES+ KA    +   G  +
Sbjct: 100 KARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKA----LALTGQML 155

Query: 170 IN----------NKKIEAKKAKAKSG------KIFVGGLSPEMKDEEIKAHFAQFGNIIE 213
           +            K   AK A  + G      K++VG L   + ++E++  F  FG+I +
Sbjct: 156 LGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIED 215

Query: 214 TEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEV-----------DVK---K 259
            ++  D    + K F FI F       + L    + +N  E+           D      
Sbjct: 216 VQLHRDPETGRSKGFGFIQFHDAEEAKEAL----EVMNGFELAGRPIKVGYAQDSTYLLD 271

Query: 260 ATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGIS 319
           A    E    +   G       R   M       G  G    G   K  L  +L   GI 
Sbjct: 272 AANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGII 331

Query: 320 GRSLVCRTGPMVQATPPLAE 339
             ++   +     A   +A 
Sbjct: 332 DPNI--PSRYATGALAIMAR 349

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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 61.6 bits (150), Expect = 4e-12
 Identities = 24/52 (46%), Positives = 34/52 (65%), Gaps = 1/52 (1%)

Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           G+  K TE +LK++FS +GE+  V +K DP TG+S+GF F+ F D E   K 
Sbjct: 6   GLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV 57

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

 Score = 68.3 bits (167), Expect = 5e-12
 Identities = 41/156 (26%), Positives = 73/156 (46%), Gaps = 24/156 (15%)

Query: 116 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN--- 172
           L + FSK+G I +  + +D N G+SRG+ F+ F+  ES + A     I + N ++ N   
Sbjct: 105 LFDTFSKFGNILSCKVATDEN-GKSRGYGFVHFEKEESAKAA-----IQKVNGMLLNDKE 158

Query: 173 --------KKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQ 224
                   K         K   ++V  L P + +++++  FA+FG I    +  D S  +
Sbjct: 159 VYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGS-GR 217

Query: 225 RKNFCFITFE-HESVVIDLLKNPKQKINDKEVDVKK 259
            + F F+ FE HE           +++N K++ + K
Sbjct: 218 SRGFAFVNFEKHEDA-----AKAVEEMNGKKIGLAK 248

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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 61.1 bits (149), Expect = 6e-12
 Identities = 25/65 (38%), Positives = 42/65 (64%), Gaps = 5/65 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           E+L+E+FS+YG +E+V + +D  TG+ RGFAF+ F D + ++K      + +  H IN  
Sbjct: 14  EDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKI-----VLQKYHTINGH 68

Query: 174 KIEAK 178
           ++E K
Sbjct: 69  RVEVK 73

This subfamily corresponds to the RRM2 of 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 = 73

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

 Score = 66.9 bits (162), Expect = 6e-12
 Identities = 47/176 (26%), Positives = 73/176 (41%), Gaps = 26/176 (14%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA--SVEDVIAEGNHVIN 171
           E+L+E F K+G ++ V L  D  TG+SRGFAF+ F+  ES EKA   +     EG  +  
Sbjct: 130 EDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRV 189

Query: 172 NKKIEAKKAKA-----------------------KSGKIFVGGLSPEMKDEEIKAHFAQF 208
            K   A + ++                       KS  ++VG L  +  +EE+   F   
Sbjct: 190 QKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSR 249

Query: 209 GNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKP 264
           G+I+   +P  K     K+  F+  E  S       +   K        +KA  +P
Sbjct: 250 GDIVRASLPPSKDGKIPKSRSFVGNEA-SKDALESNSRGNKKKILGRGPRKAFSQP 304

Length = 306

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 61.2 bits (148), Expect = 7e-12
 Identities = 26/47 (55%), Positives = 39/47 (82%)

Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           D   ++LK++FSK+GE+ + TLK DP TGRSRGF F++FK++ES++K
Sbjct: 9   DTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDK 55

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|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 = 61.1 bits (149), Expect = 7e-12
 Identities = 32/77 (41%), Positives = 45/77 (58%), Gaps = 7/77 (9%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + TE EL+  FSK+G +E V L  DP TG SRGF F+ F   ES+E A  +  I +
Sbjct: 8   GLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTF---ESVEDA--DAAIRD 62

Query: 166 GN-HVINNKKIEAKKAK 181
            N   +  + I+ +KAK
Sbjct: 63  LNGKELEGRVIKVEKAK 79

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

 Score = 60.7 bits (148), Expect = 8e-12
 Identities = 23/75 (30%), Positives = 41/75 (54%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           KIFVGGL     D+ ++ +F+QFG I E  +  D+   + + + F+TF+ +       K+
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 246 PKQKINDKEVDVKKA 260
           P   I+ ++ +V  A
Sbjct: 62  PNPIIDGRKANVNLA 76

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|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 60.5 bits (147), Expect = 9e-12
 Identities = 26/67 (38%), Positives = 37/67 (55%), Gaps = 5/67 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           E+++E+F K+G I  + L  D  T + RGF FI F   E      V+ ++    HVI  K
Sbjct: 14  EKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEE-----PVKKILETQFHVIGGK 68

Query: 174 KIEAKKA 180
           K+E KKA
Sbjct: 69  KVEVKKA 75

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, 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. It 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 memembers 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 = 75

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

 Score = 60.7 bits (148), Expect = 9e-12
 Identities = 24/44 (54%), Positives = 33/44 (75%), Gaps = 1/44 (2%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E+LK+ FSK+G IE++ +  D  TGRS+GFAF+ F+D E  EKA
Sbjct: 13  EDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKA 55

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

 Score = 60.8 bits (148), Expect = 9e-12
 Identities = 27/73 (36%), Positives = 43/73 (58%), Gaps = 6/73 (8%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +    TEE L+E FSK+GEIE+V +  D + G+S+GFAF+ F+  E  EKA    + A 
Sbjct: 5   NLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKA----LEAL 59

Query: 166 GNHVINNKKIEAK 178
               ++ +K++  
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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 60.8 bits (147), Expect = 9e-12
 Identities = 29/75 (38%), Positives = 47/75 (62%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           KIFVGGL+PE  +E+I+ +F +FG I   E+P D   ++R+ F FITF+ E  V  +L+ 
Sbjct: 6   KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLEK 65

Query: 246 PKQKINDKEVDVKKA 260
               ++  + ++K A
Sbjct: 66  KFHNVSGSKCEIKVA 80

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), 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 A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

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

 Score = 59.9 bits (146), Expect = 1e-11
 Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN- 245
           +FVG L P+  +E++K  F++FG I    +  D++  + K F F+ FE E      L+  
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETG-RSKGFAFVEFEDEEDAEKALEAL 59

Query: 246 PKQKINDKEV 255
             +++  +E+
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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 60.4 bits (147), Expect = 1e-11
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE-HESVVIDLLKN 245
           +FVG L P+  +E+++  F++FG I    +  DK   + K F F+ FE  E     L   
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDG-KSKGFAFVEFESPEDAEKALEAL 59

Query: 246 PKQKINDKEVDVK 258
             ++++ +++ 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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 59.7 bits (145), Expect = 2e-11
 Identities = 24/48 (50%), Positives = 31/48 (64%)

Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           D I   L EHFS  GEI  V++ +D  TG S+GFA+I FK  + +EKA
Sbjct: 14  DDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 59.4 bits (144), Expect = 3e-11
 Identities = 22/44 (50%), Positives = 30/44 (68%)

Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
            E L+E+FSK+GEI+   +  DP T RSRGF F+ F D  S++K
Sbjct: 12  AEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDK 55

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

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

 Score = 66.4 bits (162), Expect = 3e-11
 Identities = 40/156 (25%), Positives = 71/156 (45%), Gaps = 29/156 (18%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV-------IAEG 166
           ++L+E F+K+GEI +  +  D + GRSRGFAF+ F+  E   KA VE++         EG
Sbjct: 193 DKLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFEKHEDAAKA-VEEMNGKKIGLAKEG 250

Query: 167 NHV------------------INNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQF 208
             +                      + E +K KA+   ++V  L   + DE+++  F++ 
Sbjct: 251 KKLYVGRAQKRAEREAELRRKFEELQQE-RKMKAQGVNLYVKNLDDTVTDEKLRELFSEC 309

Query: 209 GNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK 244
           G I   ++  D+ K   + F F+ F +       + 
Sbjct: 310 GEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVT 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|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 59.3 bits (143), Expect = 3e-11
 Identities = 31/78 (39%), Positives = 51/78 (65%)

Query: 183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDL 242
           ++ KIFVGGLS     E++K +F QFG + +  + +DK+ ++ + F F+TFE+E VV  +
Sbjct: 2   RTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKV 61

Query: 243 LKNPKQKINDKEVDVKKA 260
            +    +IN+K V+ KKA
Sbjct: 62  CEIHFHEINNKMVECKKA 79

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 59.3 bits (144), Expect = 3e-11
 Identities = 21/44 (47%), Positives = 27/44 (61%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           E LK  FSKYG +  V+L    +TG  +GFAFI F+  E  +KA
Sbjct: 14  EWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKA 57

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

 Score = 59.3 bits (144), Expect = 3e-11
 Identities = 21/44 (47%), Positives = 27/44 (61%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E LK  FSKYG +  V+L    +TG  +GFAFI F+  E  +KA
Sbjct: 14  EWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKA 57

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|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 58.9 bits (142), Expect = 4e-11
 Identities = 29/74 (39%), Positives = 47/74 (63%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           KIFVGGLS     E++K +F QFG + +  + +DK+ ++ + F F+TFE E +V  + + 
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 246 PKQKINDKEVDVKK 259
              +IN+K V+ KK
Sbjct: 61  HFHEINNKMVECKK 74

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 58.4 bits (142), Expect = 5e-11
 Identities = 25/47 (53%), Positives = 32/47 (68%), Gaps = 1/47 (2%)

Query: 112 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           ITE+ L+  F  +GEIE V L+ DP TGRS+G+ FI F D E  +KA
Sbjct: 10  ITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKA 56

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

 Score = 58.4 bits (142), Expect = 5e-11
 Identities = 25/47 (53%), Positives = 32/47 (68%), Gaps = 1/47 (2%)

Query: 606 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ITE+ L+  F  +GEIE V L+ DP TGRS+G+ FI F D E  +KA
Sbjct: 10  ITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKA 56

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|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 57.8 bits (140), Expect = 9e-11
 Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 5/66 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           +++K++FS++G++E+  L  D  T R RGF F+ F+  + ++K     V     H INNK
Sbjct: 14  DDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDK-----VCEIHFHEINNK 68

Query: 174 KIEAKK 179
            +E KK
Sbjct: 69  MVECKK 74

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 57.7 bits (139), Expect = 1e-10
 Identities = 23/47 (48%), Positives = 36/47 (76%)

Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           D   ++L E+ S++GE+ + T+K+DP TGRSRGF F++FKD  S++K
Sbjct: 10  DTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDK 56

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which 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. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

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

 Score = 57.7 bits (140), Expect = 1e-10
 Identities = 25/52 (48%), Positives = 35/52 (67%), Gaps = 2/52 (3%)

Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            +    TEE L+E FSK+GEIE+V +  D + G+S+GFAF+ F+  E  EKA
Sbjct: 5   NLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKA 55

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

 Score = 57.8 bits (140), Expect = 1e-10
 Identities = 23/47 (48%), Positives = 30/47 (63%)

Query: 111 KITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
            I   L EHFS  GEI  V++ +D  TG S+GFA+I FK  + +EKA
Sbjct: 15  DIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 63.4 bits (154), Expect = 1e-10
 Identities = 40/126 (31%), Positives = 60/126 (47%), Gaps = 9/126 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           EE++  F+  GEIE+  L  D  TG+S G+ F+ +   E  EKA    V +     + NK
Sbjct: 18  EEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA----VNSLNGLRLQNK 73

Query: 174 KIEAKKAKAKSGKI-----FVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF 228
            I+   A+  S  I     +V GL   M   E+++ F+ FG II + +  D      K  
Sbjct: 74  TIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGV 133

Query: 229 CFITFE 234
            FI F+
Sbjct: 134 GFIRFD 139

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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 21/78 (26%), Positives = 44/78 (56%), Gaps = 1/78 (1%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           +IFVGG+ P+  +EE++  F++FG++ + ++  D++    K + F+TFE +     +L  
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRA-GVSKGYGFVTFETQEDAEKILAM 62

Query: 246 PKQKINDKEVDVKKATPK 263
                  K++++  A  K
Sbjct: 63  GNLNFRGKKLNIGPAIRK 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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 56.8 bits (137), Expect = 2e-10
 Identities = 23/67 (34%), Positives = 42/67 (62%), Gaps = 6/67 (8%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           + L+E+F ++GE+ + T+  D  TGRSRGF F+ FK  +S+      + + +  H+++ K
Sbjct: 13  DSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSV------NEVMKKEHILDGK 66

Query: 174 KIEAKKA 180
            I+ K+A
Sbjct: 67  IIDPKRA 73

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 = 76

>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 23/52 (44%), Positives = 38/52 (73%), Gaps = 1/52 (1%)

Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           G+ + +TEE L+E+FS+YG +E+V + +D  TG+ RGFAF+ F D + ++K 
Sbjct: 6   GLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKI 57

This subfamily corresponds to the RRM2 of 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 = 73

>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 = 56.1 bits (136), Expect = 4e-10
 Identities = 24/52 (46%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           G+  + TE EL+  FSK+G +E V L  DP TG SRGF F+ F+  E  + A
Sbjct: 8   GLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAA 59

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|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 56.2 bits (135), Expect = 4e-10
 Identities = 28/75 (37%), Positives = 47/75 (62%), Gaps = 6/75 (8%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + T+E L+E+F ++GE++   +  DP T RSRGF F+ F D     +A V+ V+A+
Sbjct: 7   GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD-----QAGVDKVLAQ 61

Query: 166 GNHVINNKKIEAKKA 180
             H +++K I+ K A
Sbjct: 62  SRHELDSKTIDPKVA 76

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 56.1 bits (135), Expect = 4e-10
 Identities = 27/69 (39%), Positives = 42/69 (60%), Gaps = 5/69 (7%)

Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK 174
           +L EHFS++G +E   + +D  TG+ RGF F+ F++ +S +KA+V        H IN  +
Sbjct: 15  DLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVKF-----HPINGHR 69

Query: 175 IEAKKAKAK 183
           +E KKA  K
Sbjct: 70  VEVKKAVPK 78

This subgroup corresponds to the RRM2 of hnRNP A0, 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 = 80

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 56.1 bits (135), Expect = 5e-10
 Identities = 29/79 (36%), Positives = 48/79 (60%), Gaps = 7/79 (8%)

Query: 107 GIVHKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIA 164
           G + + TEE  L+++F KYG+IE + +  D  +G+ RGFAF+ F D ++++K     ++ 
Sbjct: 6   GGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDK-----IVV 60

Query: 165 EGNHVINNKKIEAKKAKAK 183
           +  H IN    E KKA +K
Sbjct: 61  QKYHTINGHNCEVKKALSK 79

This subgroup corresponds to the RRM2 of hnRNP A3, 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 = 80

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

 Score = 55.7 bits (135), Expect = 6e-10
 Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 9/70 (12%)

Query: 111 KITEE-LKEHFSKYGEIENVTL--KSDPNTGRSR-GFAFIVFKDTESLEKASVEDVIAEG 166
           K+ E+ L+  FSK+GE+E++ +  K D   GR   GFAF+ FKD  S E A     +   
Sbjct: 11  KLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA-----LQLN 65

Query: 167 NHVINNKKIE 176
              +  +KI 
Sbjct: 66  GTELGGRKIS 75

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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 55.9 bits (134), Expect = 6e-10
 Identities = 28/67 (41%), Positives = 43/67 (64%), Gaps = 5/67 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           + L+++FSK+GEI    +  DP T RSRGF F+ F D      ASV+ V+A+ +H +++K
Sbjct: 14  DSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFAD-----PASVDKVLAQPHHELDSK 68

Query: 174 KIEAKKA 180
            I+ K A
Sbjct: 69  TIDPKVA 75

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 55.5 bits (134), Expect = 7e-10
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
           S ++FVG L  ++ ++E+K  F +FGN++E  +       +  NF F+ F+    V  +L
Sbjct: 3   SHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKIL 62

Query: 244 KN-PKQKINDKEVDV 257
            N P     D  ++V
Sbjct: 63  ANKPIYFRGDHRLNV 77

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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 55.4 bits (134), Expect = 7e-10
 Identities = 21/44 (47%), Positives = 28/44 (63%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           EEL+EHF   G I  +T+  D  TG+ +GFA+I F D  S+E A
Sbjct: 14  EELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENA 57

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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 55.4 bits (134), Expect = 7e-10
 Identities = 21/44 (47%), Positives = 28/44 (63%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           EEL+EHF   G I  +T+  D  TG+ +GFA+I F D  S+E A
Sbjct: 14  EELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENA 57

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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 55.6 bits (134), Expect = 8e-10
 Identities = 25/65 (38%), Positives = 37/65 (56%), Gaps = 5/65 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           E L+ +FS+YGE+ +  +  D  T RSRGF F+ FKD        V  V+A G H ++ +
Sbjct: 14  ETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD-----PNCVGTVLAGGPHTLDGR 68

Query: 174 KIEAK 178
            I+ K
Sbjct: 69  TIDPK 73

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 54.9 bits (133), Expect = 8e-10
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 6/64 (9%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
            E+L+E FS YG++E V L  + +  R RGFAF+ F   E  E A    +      V++ 
Sbjct: 12  EEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAA----LKKLNGLVLDG 65

Query: 173 KKIE 176
           + + 
Sbjct: 66  RTLR 69

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

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 54.7 bits (132), Expect = 1e-09
 Identities = 21/52 (40%), Positives = 33/52 (63%), Gaps = 1/52 (1%)

Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           G+  + T++ LK +FS++GEI +  +  DPNT RSRGF F+ F     ++ A
Sbjct: 6   GLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAA 57

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

 Score = 59.6 bits (143), Expect = 1e-09
 Identities = 21/101 (20%), Positives = 49/101 (48%), Gaps = 1/101 (0%)

Query: 167 NHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRK 226
               +      +K+K ++  +FVG L  ++ +E+++  F +FG +    +  D+   + +
Sbjct: 98  LFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSR 157

Query: 227 NFCFITFEHESVVIDLLKN-PKQKINDKEVDVKKATPKPEP 266
            F F+ FE E      ++    +++  + + V+KA P  +P
Sbjct: 158 GFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQP 198

Length = 306

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 54.8 bits (132), Expect = 1e-09
 Identities = 23/78 (29%), Positives = 46/78 (58%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+FVGGLS E   E ++ +F+Q+G +++  +  DK+ ++ + F F+ F+  + V  +L  
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 246 PKQKINDKEVDVKKATPK 263
               ++ + +D K  TP+
Sbjct: 61  GPHTLDGRTIDPKPCTPR 78

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 54.5 bits (132), Expect = 1e-09
 Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE-HESVVIDLLKN 245
           ++V  L P + +E+++  F+ +G +    +  +K +   + F F+ F   E     L K 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRP--RGFAFVEFASPEDAEAALKKL 58

Query: 246 PKQKINDKEV 255
               ++ + +
Sbjct: 59  NGLVLDGRTL 68

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

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

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 19/63 (30%), Positives = 37/63 (58%), Gaps = 5/63 (7%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
           ++ELKE+FS++G++++  +  D  TG S+G+ F+ F   + LE A  +       H++  
Sbjct: 13  SKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQ-----KHILEG 67

Query: 173 KKI 175
            K+
Sbjct: 68  NKL 70

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

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 17/44 (38%), Positives = 27/44 (61%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           E+LK+ F ++GE+ +  + +D  TGRSRGF F+  +  E    A
Sbjct: 14  EDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAA 57

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

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 17/44 (38%), Positives = 27/44 (61%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E+LK+ F ++GE+ +  + +D  TGRSRGF F+  +  E    A
Sbjct: 14  EDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAA 57

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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 54.1 bits (131), Expect = 2e-09
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 5/70 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           E+LKE F KYG+I +  +  D   G+S+GF F+ F++ E+ +KA    V       +N K
Sbjct: 16  EKLKELFGKYGKITSAKVMKDDE-GKSKGFGFVNFENHEAAQKA----VEELNGKEVNGK 70

Query: 174 KIEAKKAKAK 183
           K+   +A+ K
Sbjct: 71  KLYVGRAQKK 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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 54.1 bits (131), Expect = 2e-09
 Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA-SVEDVIAEGNHVINN 172
           EELKE FS++GE++   +  D  TG S+G AF+ FK  ES +K     D   +    ++ 
Sbjct: 15  EELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLDG 74

Query: 173 KKIEAKKA 180
           +++    A
Sbjct: 75  RRLIVTLA 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|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 20/73 (27%), Positives = 39/73 (53%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+FVG L   +  +E+K +F+QFG +    +P+DK     K + F++F     + + L+ 
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 246 PKQKINDKEVDVK 258
            K  +   ++ V+
Sbjct: 61  QKHILEGNKLQVQ 73

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

 Score = 53.7 bits (130), Expect = 3e-09
 Identities = 20/44 (45%), Positives = 27/44 (61%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           ++L+E F  +G I  V L  D  TG+SRGFAF+ F   E  E+A
Sbjct: 14  DDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERA 57

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

 Score = 53.7 bits (130), Expect = 3e-09
 Identities = 20/44 (45%), Positives = 27/44 (61%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ++L+E F  +G I  V L  D  TG+SRGFAF+ F   E  E+A
Sbjct: 14  DDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERA 57

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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 53.4 bits (128), Expect = 4e-09
 Identities = 27/80 (33%), Positives = 44/80 (55%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+FVGGL  ++ + ++  HF+QFG + + E+  DK   +++ F F+ F++          
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 246 PKQKINDKEVDVKKATPKPE 265
               IN   V+VKKA PK E
Sbjct: 61  KFHPINGHRVEVKKAVPKEE 80

This subgroup corresponds to the RRM2 of hnRNP A0, 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 = 80

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 53.5 bits (128), Expect = 4e-09
 Identities = 23/78 (29%), Positives = 42/78 (53%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           KIFVGG+  + ++  ++ +F ++G I   E+  D+   +++ F F+TF+    V  ++  
Sbjct: 2   KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61

Query: 246 PKQKINDKEVDVKKATPK 263
               IN    +VKKA  K
Sbjct: 62  KYHTINGHNCEVKKALSK 79

This subgroup corresponds to the RRM2 of hnRNP A3, 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 = 80

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 53.5 bits (128), Expect = 4e-09
 Identities = 26/76 (34%), Positives = 47/76 (61%), Gaps = 7/76 (9%)

Query: 107 GIVHKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIA 164
           G + + TEE  L+++F +YG+IE + + +D  +G+ RGFAF+ F D +S++K     ++ 
Sbjct: 6   GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK-----IVI 60

Query: 165 EGNHVINNKKIEAKKA 180
           +  H +N    E +KA
Sbjct: 61  QKYHTVNGHNCEVRKA 76

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, 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. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play 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 = 77

>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 = 53.1 bits (128), Expect = 4e-09
 Identities = 23/48 (47%), Positives = 27/48 (56%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED 161
           EEL+E F  +GEI  V L  D  T RS+GFAF+ F   E   KA  E 
Sbjct: 14  EELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

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|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 = 53.1 bits (128), Expect = 4e-09
 Identities = 23/48 (47%), Positives = 27/48 (56%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED 655
           EEL+E F  +GEI  V L  D  T RS+GFAF+ F   E   KA  E 
Sbjct: 14  EELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

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

 Score = 53.0 bits (128), Expect = 5e-09
 Identities = 23/51 (45%), Positives = 32/51 (62%), Gaps = 4/51 (7%)

Query: 605 KITEE-LKEHFSKYGEIENVTL--KSDPNTGRSR-GFAFIVFKDTESLEKA 651
           K+ E+ L+  FSK+GE+E++ +  K D   GR   GFAF+ FKD  S E A
Sbjct: 11  KLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

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

 Score = 53.0 bits (128), Expect = 5e-09
 Identities = 21/43 (48%), Positives = 29/43 (67%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           EELKE FS++GE++   +  D  TG S+G AF+ FK  ES +K
Sbjct: 15  EELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQK 57

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

 Score = 52.7 bits (127), Expect = 5e-09
 Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 5/54 (9%)

Query: 603 VDKIT-----EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           VD +T     ++L+  F KYGE+ +V +  D  T  SRGFAF+ F D    E A
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDA 56

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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 52.9 bits (127), Expect = 5e-09
 Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 5/69 (7%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
              L+ HF++YG++    +  DPNT RSRGF FI F   +  ++A     +    H I+ 
Sbjct: 16  DSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA-----MEAQPHSIDG 70

Query: 173 KKIEAKKAK 181
            +IE K+AK
Sbjct: 71  NQIELKRAK 79

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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 52.6 bits (127), Expect = 5e-09
 Identities = 16/48 (33%), Positives = 30/48 (62%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
           ++VGGL+ E+ ++ + A F  FG+I + ++P D    + + F F+ FE
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFE 48

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

 Score = 52.6 bits (127), Expect = 6e-09
 Identities = 21/44 (47%), Positives = 29/44 (65%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
            +L+E FS+YG IE V +  D  TGRSRGF F+ F+  E  ++A
Sbjct: 14  RDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEA 57

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

 Score = 52.6 bits (127), Expect = 6e-09
 Identities = 21/44 (47%), Positives = 29/44 (65%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            +L+E FS+YG IE V +  D  TGRSRGF F+ F+  E  ++A
Sbjct: 14  RDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEA 57

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|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 = 52.2 bits (126), Expect = 8e-09
 Identities = 17/48 (35%), Positives = 28/48 (58%)

Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           D   E+L E FS+ G + +  L +D +TG+ +G+ F  F+D E+   A
Sbjct: 9   DATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASA 56

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|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 52.4 bits (125), Expect = 9e-09
 Identities = 26/69 (37%), Positives = 42/69 (60%), Gaps = 5/69 (7%)

Query: 112 ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVIN 171
           + E++K++F ++G++E+  L  D  T R RGF F+ F++ + +EK     V     H IN
Sbjct: 16  VVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEK-----VCEIHFHEIN 70

Query: 172 NKKIEAKKA 180
           NK +E KKA
Sbjct: 71  NKMVECKKA 79

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

>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 = 51.6 bits (124), Expect = 1e-08
 Identities = 21/51 (41%), Positives = 34/51 (66%), Gaps = 1/51 (1%)

Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           G+   +TE E KE+FS++G++ +  L  D +TGRSRGF F+ F    ++E+
Sbjct: 6   GLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVER 56

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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 24/73 (32%), Positives = 44/73 (60%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+FVGGL  ++ +E+++ +F+Q+GN+   E+  DK   +++ F F+TF+    V  ++  
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 246 PKQKINDKEVDVK 258
               IN   V+VK
Sbjct: 61  KYHTINGHRVEVK 73

This subfamily corresponds to the RRM2 of 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 = 73

>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 = 17/49 (34%), Positives = 32/49 (65%)

Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED 655
           ++ELKE+FS++G++++  +  D  TG S+G+ F+ F   + LE A  + 
Sbjct: 13  SKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQ 61

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

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 19/44 (43%), Positives = 26/44 (59%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           ++L+  F KYGE+ +V +  D  T  SRGFAF+ F D    E A
Sbjct: 13  DDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDA 56

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|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 = 51.9 bits (125), Expect = 1e-08
 Identities = 16/45 (35%), Positives = 27/45 (60%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
            E+L E FS+ G + +  L +D +TG+ +G+ F  F+D E+   A
Sbjct: 12  EEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASA 56

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|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 52.0 bits (124), Expect = 1e-08
 Identities = 24/79 (30%), Positives = 47/79 (59%), Gaps = 7/79 (8%)

Query: 107 GIVHKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIA 164
           G + + TEE  L+++F +YG+I+ + + +D  +G+ RGF F+ F D + ++K     ++ 
Sbjct: 6   GGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDK-----IVL 60

Query: 165 EGNHVINNKKIEAKKAKAK 183
           +  H IN    E +KA ++
Sbjct: 61  QKYHTINGHNAEVRKALSR 79

This subgroup corresponds to the RRM2 of hnRNP A2/B1, 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 A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 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 = 80

>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 51.4 bits (123), Expect = 2e-08
 Identities = 18/55 (32%), Positives = 33/55 (60%)

Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF 658
           +   + L+E+F ++GE+ + T+  D  TGRSRGF F+ FK  +S+ +   ++   
Sbjct: 9   ETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKEHIL 63

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 = 76

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

 Score = 56.7 bits (137), Expect = 3e-08
 Identities = 44/171 (25%), Positives = 76/171 (44%), Gaps = 28/171 (16%)

Query: 111 KITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV 169
            +TE +L + F  +G + +V +  D  T RS G+ ++ F++    E+A    +       
Sbjct: 11  DVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERA----LETMNFKR 66

Query: 170 INNKKIEAKK-----AKAKSGK--IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYD--- 219
           +  K I         +  +SG   IFV  L   + ++ +   F++FGNI+  ++  D   
Sbjct: 67  LGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENG 126

Query: 220 KSKSQRKNFCFITFEHESVVIDLLKNPKQKIN-----DKEVDVKKATPKPE 265
           KS+     + F+ FE E      +    QK+N     DKEV V +   K E
Sbjct: 127 KSRG----YGFVHFEKEESAKAAI----QKVNGMLLNDKEVYVGRFIKKHE 169

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|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 = 50.6 bits (121), Expect = 4e-08
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 4/72 (5%)

Query: 185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK 244
           GK+F+GGLS +  ++ ++  F+++G I E  +  D+   + + F F+TFE+     D  K
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN----PDDAK 56

Query: 245 NPKQKINDKEVD 256
           +    +N K VD
Sbjct: 57  DAMMAMNGKSVD 68

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|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic polyadenylation element-binding protein CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 50.9 bits (122), Expect = 4e-08
 Identities = 24/62 (38%), Positives = 39/62 (62%), Gaps = 4/62 (6%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYD-KSKSQR--KNFCFITFEHESVVIDL 242
           K+FVGGL P++ ++EI A F +FG ++  + P+  +SKS    K + F+ F+ ES V  L
Sbjct: 2   KVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 60

Query: 243 LK 244
           + 
Sbjct: 61  ID 62

This subgroup corresponds to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and CPEB-4, all well-conserved in both, vertebrates and invertebrates. Due to the high sequence similarity, members in this family may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All family members contain an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. In addition, they do have conserved nuclear export signals that are not present in CPEB-1. . Length = 92

>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 50.1 bits (120), Expect = 5e-08
 Identities = 22/74 (29%), Positives = 42/74 (56%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           +F+GGLS +   E ++ +F++FG I E  +  D +  + + F F+TF   + V  +L   
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 247 KQKINDKEVDVKKA 260
             +++ K++D K A
Sbjct: 61  PHELDGKKIDPKVA 74

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 50.4 bits (120), Expect = 5e-08
 Identities = 25/67 (37%), Positives = 41/67 (61%), Gaps = 5/67 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           E+++E+F ++GEIE + L  DP T + RGF FI FK+ + ++K     V+ +  H ++  
Sbjct: 19  EKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKK-----VLEKKFHNVSGS 73

Query: 174 KIEAKKA 180
           K E K A
Sbjct: 74  KCEIKVA 80

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), 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 A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 50.3 bits (121), Expect = 5e-08
 Identities = 21/49 (42%), Positives = 34/49 (69%), Gaps = 2/49 (4%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV 656
           E+LKE F KYG+I +  +  D   G+S+GF F+ F++ E+ +KA VE++
Sbjct: 16  EKLKELFGKYGKITSAKVMKDDE-GKSKGFGFVNFENHEAAQKA-VEEL 62

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

 Score = 54.6 bits (130), Expect = 6e-08
 Identities = 23/44 (52%), Positives = 31/44 (70%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E+L+E F K+G ++ V L  D  TG+SRGFAF+ F+  ES EKA
Sbjct: 130 EDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKA 173

Length = 306

>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 49.9 bits (119), Expect = 7e-08
 Identities = 25/78 (32%), Positives = 47/78 (60%), Gaps = 3/78 (3%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           +F+GGL+ E  D+ ++ +F QFG + +  +  D +  + + F F+TF+    V +++K  
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMK-- 58

Query: 247 KQKIND-KEVDVKKATPK 263
           K+ I D K +D K+A P+
Sbjct: 59  KEHILDGKIIDPKRAIPR 76

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 = 76

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 49.5 bits (119), Expect = 7e-08
 Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 1/48 (2%)

Query: 111 KITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           K+ E +L E FSK G++ +V +  D N+ RS+G A++ F D ES+  A
Sbjct: 10  KVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA 57

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|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 49.5 bits (119), Expect = 7e-08
 Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 1/48 (2%)

Query: 605 KITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           K+ E +L E FSK G++ +V +  D N+ RS+G A++ F D ES+  A
Sbjct: 10  KVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA 57

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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 49.2 bits (118), Expect = 9e-08
 Identities = 20/57 (35%), Positives = 27/57 (47%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
           IFVG +      EE++ HF   G I    +  DK   Q K F +I F  +S V + L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL 58

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 49.1 bits (118), Expect = 9e-08
 Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            E+L+E FS YG++E V L  + +  R RGFAF+ F   E  E A
Sbjct: 12  EEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAA 54

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

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 55.1 bits (132), Expect = 9e-08
 Identities = 37/147 (25%), Positives = 70/147 (47%), Gaps = 25/147 (17%)

Query: 109 VHKITEELKEH-----FSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE----SLE---- 155
           V  I+ EL+E      F  +G I+++ +  DP TG+ +GFAF+ ++  E    +LE    
Sbjct: 112 VGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNG 171

Query: 156 --------KASVEDVIAEGNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQ 207
                   K      + +   +I+  + EAKK      +I+V  + P++ + +IK+ F  
Sbjct: 172 QMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFN----RIYVASVHPDLSETDIKSVFEA 227

Query: 208 FGNIIETEMPYDKSKSQRKNFCFITFE 234
           FG I++ ++    +    K + FI + 
Sbjct: 228 FGEIVKCQLARAPTGRGHKGYGFIEYN 254

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|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 17/44 (38%), Positives = 26/44 (59%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E+++E+F K+G I  + L  D  T + RGF FI F   E ++K 
Sbjct: 14  EKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKI 57

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, 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. It 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 memembers 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 = 75

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 49.2 bits (117), Expect = 1e-07
 Identities = 23/75 (30%), Positives = 45/75 (60%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+FVGGLS +   +++K +F +FG + +  +  D +  + + F FI F+  S V  +L+ 
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 246 PKQKINDKEVDVKKA 260
            + +++ + +D KKA
Sbjct: 61  KEHRLDGRLIDPKKA 75

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which 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 A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 49.2 bits (117), Expect = 1e-07
 Identities = 28/75 (37%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+    TEE +KE+F  +GEIEN+ L  D  T   RGF F+ + D E ++K     ++  
Sbjct: 6   GLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQK-----LLES 60

Query: 166 GNHVINNKKIEAKKA 180
             H I + K E K A
Sbjct: 61  RYHQIGSGKCEIKVA 75

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), 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. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . 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 = 49.1 bits (118), Expect = 1e-07
 Identities = 18/50 (36%), Positives = 30/50 (60%)

Query: 185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
            K+FV GLS    ++E++A F++FG + E  +  D    + + F F+TFE
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFE 51

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|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 49.2 bits (117), Expect = 1e-07
 Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 5/71 (7%)

Query: 109 VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH 168
           V+   E++K++F ++G++++  L  D  T R RGF F+ F+  + +EK     V     H
Sbjct: 9   VNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK-----VCEIHFH 63

Query: 169 VINNKKIEAKK 179
            INNK +E KK
Sbjct: 64  EINNKMVECKK 74

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 49.1 bits (117), Expect = 1e-07
 Identities = 21/54 (38%), Positives = 36/54 (66%), Gaps = 1/54 (1%)

Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASV 653
           G+   + E +L EHFS++G +E   + +D  TG+ RGF F+ F++ +S +KA+V
Sbjct: 6   GLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAV 59

This subgroup corresponds to the RRM2 of hnRNP A0, 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 = 80

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 48.9 bits (116), Expect = 1e-07
 Identities = 20/43 (46%), Positives = 29/43 (67%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           + L+++FSK+GEI    +  DP T RSRGF F+ F D  S++K
Sbjct: 14  DSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDK 56

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 49.0 bits (117), Expect = 1e-07
 Identities = 18/37 (48%), Positives = 25/37 (67%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKD 644
           E L+ +FS+YGE+ +  +  D  T RSRGF F+ FKD
Sbjct: 14  ETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD 50

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

 Score = 49.1 bits (118), Expect = 1e-07
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           EEL++HF   G++E V +  D  TG  +GF +++FK  +S+  A     +      +  +
Sbjct: 14  EELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALA-----LKLNGIKLKGR 68

Query: 174 KI 175
           KI
Sbjct: 69  KI 70

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

 Score = 49.1 bits (118), Expect = 1e-07
 Identities = 17/44 (38%), Positives = 28/44 (63%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           EEL++HF   G++E V +  D  TG  +GF +++FK  +S+  A
Sbjct: 14  EELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALA 57

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 49.3 bits (117), Expect = 1e-07
 Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 5/70 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           E L+ HF ++G + +  +  DPNT RSRGF F+ +   E ++ A     +    H ++ +
Sbjct: 17  ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA-----MNARPHKVDGR 71

Query: 174 KIEAKKAKAK 183
            +E K+A ++
Sbjct: 72  VVEPKRAVSR 81

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

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 25/67 (37%), Positives = 35/67 (52%), Gaps = 11/67 (16%)

Query: 111 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV 169
           K TE  LK+ FS +G +  VT+   P  G+ +GFAF+ F      EKA ++ V       
Sbjct: 10  KCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKA-IKGV------- 60

Query: 170 INNKKIE 176
            N KKI+
Sbjct: 61  -NGKKIK 66

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

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 20/48 (41%), Positives = 27/48 (56%), Gaps = 2/48 (4%)

Query: 605 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           K TE  LK+ FS +G +  VT+   P  G+ +GFAF+ F      EKA
Sbjct: 10  KCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKA 56

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|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 = 49.1 bits (118), Expect = 1e-07
 Identities = 19/44 (43%), Positives = 29/44 (65%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           E+++  F +YG IE VT+  D +TG+S+G AF+ F   E  +KA
Sbjct: 14  EDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKA 57

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|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 = 49.1 bits (118), Expect = 1e-07
 Identities = 19/44 (43%), Positives = 29/44 (65%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E+++  F +YG IE VT+  D +TG+S+G AF+ F   E  +KA
Sbjct: 14  EDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKA 57

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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 48.5 bits (115), Expect = 2e-07
 Identities = 22/51 (43%), Positives = 31/51 (60%), Gaps = 1/51 (1%)

Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           G+    TEE +KE+F  +GEIEN+ L  D  T   RGF F+ + D E ++K
Sbjct: 6   GLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQK 56

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), 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. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 53.4 bits (128), Expect = 2e-07
 Identities = 25/52 (48%), Positives = 34/52 (65%), Gaps = 1/52 (1%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
            +   ITE EL++ F  +G+IE+V L  DP TGRS+GF FI F D E  ++A
Sbjct: 193 NLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA 244

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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 48.5 bits (115), Expect = 2e-07
 Identities = 23/75 (30%), Positives = 43/75 (57%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+F+GGLS +   + ++ +F++FG I E  +  D +  + + F F+TF   + V  +L  
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 246 PKQKINDKEVDVKKA 260
           P  +++ K +D K A
Sbjct: 61  PHHELDSKTIDPKVA 75

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 49.2 bits (118), Expect = 2e-07
 Identities = 16/43 (37%), Positives = 26/43 (60%)

Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           +L+  F +YG I+ + L  D  TG+ RG+AFI F+    ++ A
Sbjct: 17  KLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAA 59

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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 49.2 bits (118), Expect = 2e-07
 Identities = 16/43 (37%), Positives = 26/43 (60%)

Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +L+  F +YG I+ + L  D  TG+ RG+AFI F+    ++ A
Sbjct: 17  KLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAA 59

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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 48.3 bits (116), Expect = 2e-07
 Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 112 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           + ++ LKE FS YG +++V L  D      RG+A++ F+  E  EKA
Sbjct: 10  VNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKA 56

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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 48.3 bits (116), Expect = 2e-07
 Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 606 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           + ++ LKE FS YG +++V L  D      RG+A++ F+  E  EKA
Sbjct: 10  VNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKA 56

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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 25/53 (47%), Positives = 35/53 (66%), Gaps = 1/53 (1%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 158
           GI +  TE E++ +FS  GEIE + L + P+TGR RG AFI FK  E+ ++A 
Sbjct: 5   GIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL 57

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 48.2 bits (115), Expect = 3e-07
 Identities = 15/44 (34%), Positives = 30/44 (68%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +++K++FS++G++E+  L  D  T R RGF F+ F+  + ++K 
Sbjct: 14  DDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKV 57

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 53.0 bits (127), Expect = 3e-07
 Identities = 25/47 (53%), Positives = 33/47 (70%), Gaps = 1/47 (2%)

Query: 606 ITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ITE EL++ F  +G+IE+V L  DP TGRS+GF FI F D E  ++A
Sbjct: 198 ITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA 244

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|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 47.8 bits (114), Expect = 3e-07
 Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 5/72 (6%)

Query: 110 HKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA-SVEDVIAEGN 167
           H ITE ELKE F ++G +  V + S    GR   F F+VF D E+++K  + + +   G+
Sbjct: 13  HDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANKPIYFRGD 72

Query: 168 HVINNKKIEAKK 179
           H +N   +E KK
Sbjct: 73  HRLN---VEEKK 81

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

 Score = 48.2 bits (115), Expect = 3e-07
 Identities = 19/47 (40%), Positives = 32/47 (68%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
           ++L++ FSK+GE+  V +  D  +G+S+GFA+++F D E   KA  E
Sbjct: 17  DDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

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

 Score = 48.2 bits (115), Expect = 3e-07
 Identities = 19/47 (40%), Positives = 32/47 (68%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           ++L++ FSK+GE+  V +  D  +G+S+GFA+++F D E   KA  E
Sbjct: 17  DDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 48.4 bits (116), Expect = 3e-07
 Identities = 17/34 (50%), Positives = 25/34 (73%)

Query: 120 FSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
           FS+YGEI ++ L  D  TG+S+GFAF+ ++D  S
Sbjct: 30  FSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRS 63

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 48.4 bits (116), Expect = 3e-07
 Identities = 17/34 (50%), Positives = 25/34 (73%)

Query: 614 FSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
           FS+YGEI ++ L  D  TG+S+GFAF+ ++D  S
Sbjct: 30  FSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRS 63

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

 Score = 48.0 bits (115), Expect = 3e-07
 Identities = 19/67 (28%), Positives = 39/67 (58%), Gaps = 8/67 (11%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE--GNHVIN 171
            EL+++FS++G +  + L     TG+S+G+AF+ F+  E      V  ++AE   N+++ 
Sbjct: 14  PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPE------VAKIVAETMNNYLLF 67

Query: 172 NKKIEAK 178
            + ++ K
Sbjct: 68  ERLLKCK 74

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|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 47.7 bits (113), Expect = 4e-07
 Identities = 21/75 (28%), Positives = 41/75 (54%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           KIFVGG+  + ++  ++ +F Q+G I   E+  D+   +++ F F+TF+    V  ++  
Sbjct: 2   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 61

Query: 246 PKQKINDKEVDVKKA 260
               +N    +V+KA
Sbjct: 62  KYHTVNGHNCEVRKA 76

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, 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. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play 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 = 77

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 15/47 (31%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE 646
           G+ +++ E+ L   F  +G+I+++ +  D  T + RGFAF+ F++ E
Sbjct: 5   GLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPE 51

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

 Score = 47.3 bits (113), Expect = 4e-07
 Identities = 18/45 (40%), Positives = 26/45 (57%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
            E+L  HF   G   +V L +D  TG+S+G AF+ F   E++ KA
Sbjct: 14  AEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKA 58

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

 Score = 47.3 bits (113), Expect = 4e-07
 Identities = 18/45 (40%), Positives = 26/45 (57%)

Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            E+L  HF   G   +V L +D  TG+S+G AF+ F   E++ KA
Sbjct: 14  AEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKA 58

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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 47.8 bits (113), Expect = 4e-07
 Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 5/70 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           + L+EHF K+G + +  +  DP T RSRGF F+ +   E ++ A     ++   H ++ +
Sbjct: 17  DSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA-----MSARPHKVDGR 71

Query: 174 KIEAKKAKAK 183
            +E K+A ++
Sbjct: 72  VVEPKRAVSR 81

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|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 47.3 bits (112), Expect = 5e-07
 Identities = 20/74 (27%), Positives = 43/74 (58%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           +F+GGLS +   +++K +F++FG +++  +  D    + + F F+ F+    V  ++   
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 247 KQKINDKEVDVKKA 260
           + K+N K +D K+A
Sbjct: 61  EHKLNGKVIDPKRA 74

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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 47.3 bits (112), Expect = 5e-07
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           E+++E+F ++GEIE + L  DP T + RGF FI FK+ + ++K
Sbjct: 19  EKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKK 61

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), 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 A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 47.4 bits (112), Expect = 5e-07
 Identities = 20/78 (25%), Positives = 42/78 (53%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+FVGG+  + ++  ++ +F ++G I   E+  D+   +++ F F+TF+    V  ++  
Sbjct: 2   KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61

Query: 246 PKQKINDKEVDVKKATPK 263
               IN    +V+KA  +
Sbjct: 62  KYHTINGHNAEVRKALSR 79

This subgroup corresponds to the RRM2 of hnRNP A2/B1, 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 A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 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 = 80

>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 47.4 bits (112), Expect = 5e-07
 Identities = 22/78 (28%), Positives = 43/78 (55%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+F+GGLS E  DE +++HF Q+G + +  +  D +  + + F F+T+     V   +  
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

Query: 246 PKQKINDKEVDVKKATPK 263
              K++ + V+ K+A  +
Sbjct: 64  RPHKVDGRVVEPKRAVSR 81

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|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 46.9 bits (111), Expect = 6e-07
 Identities = 21/56 (37%), Positives = 39/56 (69%), Gaps = 2/56 (3%)

Query: 601 GIVDKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           G + + TEE  L+++F +YG+IE + + +D  +G+ RGFAF+ F D +S++K  ++
Sbjct: 6   GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 61

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, 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. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play 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 = 77

>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 46.7 bits (111), Expect = 7e-07
 Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 4/65 (6%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           +ELK++FS++G ++NV +     TG S+ + FI F + E    A+     +  N+++  K
Sbjct: 14  KELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAK----SMNNYLLMGK 69

Query: 174 KIEAK 178
            ++  
Sbjct: 70  VLQVH 74

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|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 47.3 bits (113), Expect = 7e-07
 Identities = 20/64 (31%), Positives = 37/64 (57%), Gaps = 3/64 (4%)

Query: 110 HKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE--DVIAEG 166
            + TEE L+E FS+YG+I  + L  D  TG S+G+AF+ ++      +A  +   ++ +G
Sbjct: 13  LQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVIDG 72

Query: 167 NHVI 170
           + + 
Sbjct: 73  SEIF 76

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|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 46.9 bits (111), Expect = 8e-07
 Identities = 23/75 (30%), Positives = 42/75 (56%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+F+GGLS +   E ++ +F QFG + E  +  D    + + F F+TF  ++ V  +L  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 246 PKQKINDKEVDVKKA 260
            + +++ K +D K A
Sbjct: 62  SRHELDSKTIDPKVA 76

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . 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 = 46.8 bits (111), Expect = 8e-07
 Identities = 18/44 (40%), Positives = 28/44 (63%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           + L++ FSKYG+I  V +  D  T RSRGF F+ F++ +  + A
Sbjct: 15  QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDA 58

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|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 = 46.8 bits (111), Expect = 8e-07
 Identities = 18/44 (40%), Positives = 28/44 (63%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           + L++ FSKYG+I  V +  D  T RSRGF F+ F++ +  + A
Sbjct: 15  QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDA 58

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

 Score = 46.9 bits (112), Expect = 8e-07
 Identities = 24/83 (28%), Positives = 34/83 (40%), Gaps = 20/83 (24%)

Query: 111 KITE-ELKEHFSKYGEIENVT---LKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEG 166
           ++TE  L + FSKYG+I+       KS P  G+ RG+ F+ F+  E  EKA         
Sbjct: 10  RLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA--------- 60

Query: 167 NHVINNKKIEAKKAKAKSGKIFV 189
                          A   K+ V
Sbjct: 61  -------LKSLNGKTALGKKLVV 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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 46.5 bits (110), Expect = 9e-07
 Identities = 22/56 (39%), Positives = 38/56 (67%), Gaps = 2/56 (3%)

Query: 601 GIVDKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           G + + TEE  L+++F KYG+IE + +  D  +G+ RGFAF+ F D ++++K  V+
Sbjct: 6   GGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61

This subgroup corresponds to the RRM2 of hnRNP A3, 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 = 80

>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 = 46.9 bits (112), Expect = 9e-07
 Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 607 TEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           TEE L+E FS+YG+I  + L  D  TG S+G+AF+ ++      +A  +
Sbjct: 16  TEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

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|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 46.5 bits (110), Expect = 1e-06
 Identities = 18/43 (41%), Positives = 28/43 (65%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           E L+E+F ++GE++   +  DP T RSRGF F+ F D   ++K
Sbjct: 15  EGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 57

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 45.9 bits (109), Expect = 1e-06
 Identities = 18/45 (40%), Positives = 27/45 (60%)

Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
              L+ HF++YG++    +  DPNT RSRGF FI F   +  ++A
Sbjct: 16  DSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 46.6 bits (110), Expect = 1e-06
 Identities = 17/44 (38%), Positives = 27/44 (61%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E L+ HF ++G + +  +  DPNT RSRGF F+ +   E ++ A
Sbjct: 17  ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA 60

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

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 21/51 (41%), Positives = 30/51 (58%), Gaps = 4/51 (7%)

Query: 605 KITE-ELKEHFSKYGEIENVT---LKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ++TE  L + FSKYG+I+       KS P  G+ RG+ F+ F+  E  EKA
Sbjct: 10  RLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 17/52 (32%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           G+   +TE +L+++FS++G +  V +  D    R RGF FI F+  +S+++ 
Sbjct: 9   GLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 20/74 (27%), Positives = 44/74 (59%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           +FVGGLS +   +++K +F++FG +++  +  D    + + F F+ F+  + V  +L   
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 247 KQKINDKEVDVKKA 260
           + K++ + +D K+A
Sbjct: 61  EHKLDGRVIDPKRA 74

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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 25/53 (47%), Positives = 34/53 (64%), Gaps = 1/53 (1%)

Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 652
           GI    TE E++ +FS  GEIE + L + P+TGR RG AFI FK  E+ ++A 
Sbjct: 5   GIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL 57

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 6/76 (7%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+FVG L+ +M +E+++ +F+QFG + +  +P        + F F+TF    V   L   
Sbjct: 2   KVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVAQSLCGE 56

Query: 246 PKQKINDKEVDVKKAT 261
               I    V V  A 
Sbjct: 57  -DHIIKGVSVHVSNAE 71

This subfamily corresponds to the RRM2 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 = 71

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 5/57 (8%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV 169
            E+L+++FS++GE+ +V +         R FAF+ F D E  +    ED I +G  V
Sbjct: 14  EEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQSLCGEDHIIKGVSV 65

This subfamily corresponds to the RRM2 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 = 71

>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 2/49 (4%)

Query: 604 DKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            ++TEE L E F + G +E V +  DPN G+ + FAF+ FK   S+  A
Sbjct: 11  ARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYA 58

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 20/46 (43%), Positives = 27/46 (58%)

Query: 112 ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           + E L   F K G IE V +  DP T   +GFA++ FKD  ++EKA
Sbjct: 12  VEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKA 57

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 20/46 (43%), Positives = 27/46 (58%)

Query: 606 ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           + E L   F K G IE V +  DP T   +GFA++ FKD  ++EKA
Sbjct: 12  VEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKA 57

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . 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 = 45.3 bits (108), Expect = 2e-06
 Identities = 23/46 (50%), Positives = 28/46 (60%), Gaps = 2/46 (4%)

Query: 113 TEELKEHFSK-YGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
             ELKEHFSK  GEI +V L    + G+SR  AFI +K  E  +KA
Sbjct: 14  EAELKEHFSKHGGEITDVKLLRTED-GKSRRIAFIGYKTEEEAQKA 58

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|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 = 45.3 bits (108), Expect = 2e-06
 Identities = 23/46 (50%), Positives = 28/46 (60%), Gaps = 2/46 (4%)

Query: 607 TEELKEHFSK-YGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
             ELKEHFSK  GEI +V L    + G+SR  AFI +K  E  +KA
Sbjct: 14  EAELKEHFSKHGGEITDVKLLRTED-GKSRRIAFIGYKTEEEAQKA 58

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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 45.4 bits (108), Expect = 3e-06
 Identities = 24/60 (40%), Positives = 31/60 (51%), Gaps = 8/60 (13%)

Query: 437 VTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP 496
           VTE V M        YD  K + + F FITFE E  V  ++      IN K+V+VK+A P
Sbjct: 29  VTEVVVM--------YDHEKKRPRGFGFITFESEDSVDQVVNEHFHDINGKKVEVKRAEP 80

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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 15/47 (31%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE 152
           G+  ++ E+ L   F  +G+I+++ +  D  T + RGFAF+ F++ E
Sbjct: 5   GLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPE 51

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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 2/48 (4%)

Query: 111 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           ++TEE L E F + G +E V +  DPN G+ + FAF+ FK   S+  A
Sbjct: 12  RVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYA 58

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

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

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 15/50 (30%), Positives = 29/50 (58%)

Query: 185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
            +++VG +S E+ ++ I+  F+ FG I   +M +D    + K F F+ +E
Sbjct: 1   CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYE 50

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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 45.5 bits (107), Expect = 3e-06
 Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 6/78 (7%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + TEE L+ ++ ++G++ +  +  DP + RSRGF F+ F          V+  +A 
Sbjct: 9   GLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCM-----NEVDAAMAA 63

Query: 166 GNHVINNKKIEAKKAKAK 183
             H I+ + +E K+A A+
Sbjct: 64  RPHTIDGRVVEPKRAVAR 81

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which 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 A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 16/44 (36%), Positives = 24/44 (54%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           EEL+  F   G IE+  +  D  TG+S G+ F+ + D    +KA
Sbjct: 15  EELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKA 58

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

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 16/44 (36%), Positives = 24/44 (54%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           EEL+  F   G IE+  +  D  TG+S G+ F+ + D    +KA
Sbjct: 15  EELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKA 58

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|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 = 3e-06
 Identities = 25/75 (33%), Positives = 36/75 (48%), Gaps = 16/75 (21%)

Query: 109 VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH 168
           +HKI       FSKYG++  VT+  D  T +S+G AFI+F D E   K            
Sbjct: 18  LHKI-------FSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV---------K 61

Query: 169 VINNKKIEAKKAKAK 183
            +NNK++  +  K  
Sbjct: 62  ALNNKELFGRTLKCS 76

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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 45.0 bits (107), Expect = 4e-06
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 7/75 (9%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           GI    TE EL++ FS++G +++V + +D   G S+G+ F+ F+  E  EK     ++A 
Sbjct: 9   GIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEK-----ILAM 62

Query: 166 GNHVINNKKIEAKKA 180
           GN     KK+    A
Sbjct: 63  GNLNFRGKKLNIGPA 77

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|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 = 44.6 bits (106), Expect = 4e-06
 Identities = 17/49 (34%), Positives = 26/49 (53%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
           ++FV  L     +EE++  F  FG I E  +P DK   + K F F++F 
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFM 49

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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 44.8 bits (106), Expect = 4e-06
 Identities = 20/75 (26%), Positives = 41/75 (54%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+FVGGL+ +  D  ++ HF ++G + E  +  D +  + + F FITF       + ++ 
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63

Query: 246 PKQKINDKEVDVKKA 260
               I+  ++++K+A
Sbjct: 64  QPHSIDGNQIELKRA 78

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

 Score = 44.7 bits (106), Expect = 4e-06
 Identities = 19/47 (40%), Positives = 28/47 (59%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
           IFVG LSPE+  E ++A FA FG I +  +  D    + K + F++F
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSF 48

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|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 2/52 (3%)

Query: 604 DKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           D I +E L+E FS +G I +  + +D   GRS+GF F+ F   E   KA  E
Sbjct: 11  DSIDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTE 61

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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 44.7 bits (105), Expect = 5e-06
 Identities = 17/44 (38%), Positives = 27/44 (61%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           + L+EHF K+G + +  +  DP T RSRGF F+ +   E ++ A
Sbjct: 17  DSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60

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|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 44.9 bits (107), Expect = 5e-06
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 8/74 (10%)

Query: 107 GIVHKITEE-LKEHFSKYG--EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS--VED 161
           G+    TEE + +  S      I++V L  D  TG SRGFAF+ F    SLE A+  ++ 
Sbjct: 9   GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEF---PSLEDATQWMDA 65

Query: 162 VIAEGNHVINNKKI 175
           +      VI+ + +
Sbjct: 66  LNNLDPFVIDGRVV 79

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It 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. All family members 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 = 84

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 3/52 (5%)

Query: 600 PGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           P  V +  + L+EHF   GE+ +V +    + G+SR F F+ FK  E  ++A
Sbjct: 9   PKYVTE--DRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQA 57

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|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           + L+EHF   GE+ +V +    + G+SR F F+ FK  E  ++A
Sbjct: 15  DRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQA 57

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 48.9 bits (116), Expect = 5e-06
 Identities = 45/191 (23%), Positives = 75/191 (39%), Gaps = 18/191 (9%)

Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVF-KDTESLEKASVEDVIAEGNHVINNK 173
           EL   F   G I    +  D  TG S G+AF+ F  + +S       + I      + NK
Sbjct: 123 ELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGIT-----VRNK 177

Query: 174 KIEAKKAKA-----KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF 228
           +++   A+      K   ++V  L   + D+++   F ++G I++  +  DK     +  
Sbjct: 178 RLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGV 237

Query: 229 CFITF---EHESVVIDLLKNPKQKINDKEVDVKKA----TPKPEPFGVRGGRGGRGGRGG 281
            F+ F   E     I  L N   +   + + V+ A      K   +  + G G  G  G 
Sbjct: 238 AFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKAKAHHYMSQMGHGNMGNMGH 297

Query: 282 RGGRMAGGYGG 292
               MAGG G 
Sbjct: 298 GNMGMAGGSGM 308

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|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 44.2 bits (104), Expect = 6e-06
 Identities = 19/47 (40%), Positives = 31/47 (65%)

Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           D   E+++E+F  +GE+E++ L  D  T + RGF FI FK+ E ++K
Sbjct: 10  DTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 56

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, 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 = 75

>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 44.2 bits (104), Expect = 6e-06
 Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 5/67 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           E+++E+F  +GE+E++ L  D  T + RGF FI FK+ E ++K     ++ +  H +   
Sbjct: 14  EKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK-----IMEKKYHNVGLS 68

Query: 174 KIEAKKA 180
           K E K A
Sbjct: 69  KCEIKVA 75

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, 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 = 75

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 44.3 bits (104), Expect = 6e-06
 Identities = 18/56 (32%), Positives = 38/56 (67%), Gaps = 2/56 (3%)

Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY 659
           + + E++K++F ++G++E+  L  D  T R RGF F+ F++ + +EK  V +++F+
Sbjct: 14  NTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEK--VCEIHFH 67

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 44.3 bits (104), Expect = 6e-06
 Identities = 18/52 (34%), Positives = 35/52 (67%), Gaps = 2/52 (3%)

Query: 601 GIVDKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           G + + TEE  L+++F +YG+I+ + + +D  +G+ RGF F+ F D + ++K
Sbjct: 6   GGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDK 57

This subgroup corresponds to the RRM2 of hnRNP A2/B1, 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 A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 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 = 80

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

 Score = 44.3 bits (105), Expect = 6e-06
 Identities = 17/45 (37%), Positives = 26/45 (57%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           TE L+  F+ +GEI +  +  D  TG+S+G+ F+ F   E  E A
Sbjct: 13  TETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENA 57

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

 Score = 44.3 bits (105), Expect = 6e-06
 Identities = 17/45 (37%), Positives = 26/45 (57%)

Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           TE L+  F+ +GEI +  +  D  TG+S+G+ F+ F   E  E A
Sbjct: 13  TETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENA 57

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|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 44.5 bits (106), Expect = 6e-06
 Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
           E L+E FS +G I +  + +D   GRS+GF F+ F   E   KA  E
Sbjct: 16  ERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTE 61

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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 44.0 bits (104), Expect = 7e-06
 Identities = 16/45 (35%), Positives = 28/45 (62%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 652
           +ELK++FS++G ++NV +     TG S+ + FI F + E    A+
Sbjct: 14  KELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAA 58

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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 44.3 bits (104), Expect = 8e-06
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           +L+E FSKYG I +V++  D  + RSRGFAF+ F++ +  ++A
Sbjct: 25  DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 44.3 bits (104), Expect = 8e-06
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +L+E FSKYG I +V++  D  + RSRGFAF+ F++ +  ++A
Sbjct: 25  DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 43.6 bits (103), Expect = 8e-06
 Identities = 20/66 (30%), Positives = 30/66 (45%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           +FVG LS E  ++E++AHF + G I    M   +   + K F F+ FE      + LK  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

Query: 247 KQKIND 252
                 
Sbjct: 61  HLNGRA 66

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

 Score = 48.3 bits (115), Expect = 9e-06
 Identities = 22/49 (44%), Positives = 34/49 (69%), Gaps = 2/49 (4%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV 656
           ++L+E F+K+GEI +  +  D + GRSRGFAF+ F+  E   KA VE++
Sbjct: 193 DKLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFEKHEDAAKA-VEEM 239

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|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 43.8 bits (104), Expect = 9e-06
 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 2/48 (4%)

Query: 111 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
            I E+ L++ F  +G I +V LK   + G+ R F F+ +K  E  +KA
Sbjct: 11  GIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKA 57

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|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 43.8 bits (104), Expect = 9e-06
 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 2/48 (4%)

Query: 605 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            I E+ L++ F  +G I +V LK   + G+ R F F+ +K  E  +KA
Sbjct: 11  GIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKA 57

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|219320 pfam07172, GRP, Glycine rich protein family

 Score = 44.4 bits (105), Expect = 9e-06
 Identities = 21/35 (60%), Positives = 21/35 (60%)

Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
           G  GG GG G  GG GG   GG G  GG GGGYGG
Sbjct: 55  GGGGGYGGGGYYGGGGGYGGGGGGYPGGGGGGYGG 89

This family of proteins includes several glycine rich proteins as well as two nodulins 16 and 24. The family also contains proteins that are induced in response to various stresses. Length = 91

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

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 9/82 (10%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            ++VG L   + +E++K  F QFG +    +  D+   + + F F+  E        ++ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIE- 59

Query: 246 PKQKINDKEVD-----VKKATP 262
              K+N  +       V +A P
Sbjct: 60  ---KLNGTDFGGRTLTVNEARP 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|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 14/39 (35%), Positives = 26/39 (66%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE 646
            EL+++FS++G +  + L     TG+S+G+AF+ F+  E
Sbjct: 14  PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPE 52

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|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 = 43.8 bits (104), Expect = 1e-05
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 9/77 (11%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+ + ++E+ +KE    +G+++   L  D  TG S+G+AF  + D       SV D    
Sbjct: 7   GLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDP------SVTDQAIA 60

Query: 166 G--NHVINNKKIEAKKA 180
           G     + +KK+  ++A
Sbjct: 61  GLNGMQLGDKKLTVQRA 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|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 = 43.4 bits (103), Expect = 1e-05
 Identities = 13/44 (29%), Positives = 27/44 (61%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           ++L + F+ +G + +  +  D NTG+S+ F F+ + + ES + A
Sbjct: 13  QDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAA 56

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|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 = 43.4 bits (103), Expect = 1e-05
 Identities = 13/44 (29%), Positives = 27/44 (61%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ++L + F+ +G + +  +  D NTG+S+ F F+ + + ES + A
Sbjct: 13  QDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAA 56

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

 Score = 43.9 bits (104), Expect = 1e-05
 Identities = 18/44 (40%), Positives = 26/44 (59%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           ++L+  F KYG I +V +  D  T R RGFA++ F+D    E A
Sbjct: 15  DDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDA 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|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 43.9 bits (104), Expect = 1e-05
 Identities = 18/44 (40%), Positives = 26/44 (59%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ++L+  F KYG I +V +  D  T R RGFA++ F+D    E A
Sbjct: 15  DDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDA 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|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 19/44 (43%), Positives = 27/44 (61%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           +E++  FS  GEIE+  L  D  TG+S G+ F+ + D E  EKA
Sbjct: 16  DEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKA 59

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

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 19/44 (43%), Positives = 27/44 (61%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +E++  FS  GEIE+  L  D  TG+S G+ F+ + D E  EKA
Sbjct: 16  DEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKA 59

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

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 9/68 (13%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           E+L + FS    I++  + +DP TG SRG+ F+ F   E  ++A  +         + NK
Sbjct: 14  EDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK---------LKNK 64

Query: 174 KIEAKKAK 181
           K+  +  +
Sbjct: 65  KLHGRILR 72

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

 Score = 47.1 bits (112), Expect = 2e-05
 Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 2/52 (3%)

Query: 604 DKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           D +T+E L+E FS+ GEI +  +  D   G SRGF F+ F + E   +A  E
Sbjct: 295 DTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTE 345

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|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 18/57 (31%), Positives = 37/57 (64%), Gaps = 2/57 (3%)

Query: 603 VDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY 659
           V+   E++K++F ++G++++  L  D  T R RGF F+ F+  + +EK  V +++F+
Sbjct: 9   VNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK--VCEIHFH 63

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 43.2 bits (102), Expect = 2e-05
 Identities = 17/44 (38%), Positives = 26/44 (59%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +ELKE F ++G +  V + S    GR   F F+VF D E+++K 
Sbjct: 18  DELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 17/51 (33%), Positives = 30/51 (58%)

Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
           S  I++GGL  E+ + +I   F+Q+G I++  +  DK   + K F F+ +E
Sbjct: 9   SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYE 59

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|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 5/49 (10%)

Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED 655
            E+L+++FS++GE+ +V +         R FAF+ F D E  +    ED
Sbjct: 14  EEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQSLCGED 57

This subfamily corresponds to the RRM2 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 = 71

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

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 112 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
             E+ + E F +YGEI +V L +DP++GR +GF ++ F   E+ + A
Sbjct: 10  ADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAA 56

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

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 606 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
             E+ + E F +YGEI +V L +DP++GR +GF ++ F   E+ + A
Sbjct: 10  ADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAA 56

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|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 19/44 (43%), Positives = 26/44 (59%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           EEL+ HF   G +  VT+  D  +G  +GFA+I F D ES+  A
Sbjct: 14  EELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTA 57

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 19/44 (43%), Positives = 26/44 (59%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           EEL+ HF   G +  VT+  D  +G  +GFA+I F D ES+  A
Sbjct: 14  EELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTA 57

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 43.0 bits (101), Expect = 2e-05
 Identities = 19/43 (44%), Positives = 29/43 (67%)

Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           +L+E FS+YG +  V +  D  TGRSRGFAF+ F+  +  ++A
Sbjct: 15  DLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEA 57

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|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 43.0 bits (101), Expect = 2e-05
 Identities = 19/43 (44%), Positives = 29/43 (67%)

Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +L+E FS+YG +  V +  D  TGRSRGFAF+ F+  +  ++A
Sbjct: 15  DLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEA 57

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

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 3/55 (5%)

Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF---EH 235
           SG++F+  L+    +E+++  F+++G + E  +P DK   + K F F+T+   EH
Sbjct: 2   SGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEH 56

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|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis thaliana zinc finger CCCH domain-containing protein 46 (AtC3H46) and similar proteins

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 5/66 (7%)

Query: 194 PEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL-KNPKQKIND 252
               +E++  +F QFG +++  +PY     Q++ F F+TFE+   V  +L K     I  
Sbjct: 9   SRFTEEDVSEYFGQFGPVLDVRIPY----QQKRMFGFVTFENAETVKRILSKGNPHFICG 64

Query: 253 KEVDVK 258
             V VK
Sbjct: 65  SRVRVK 70

This subfamily corresponds to the RRM domain in AtC3H46, a putative RNA-binding protein that contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCCH class of zinc finger, typically C-X8-C-X5-C-X3-H. It may possess ribonuclease activity. . Length = 70

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

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 18/44 (40%), Positives = 26/44 (59%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           E LK  F K+G +    + +D  TGRSRGF ++ F+  E  +KA
Sbjct: 14  EWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKA 57

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

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 18/44 (40%), Positives = 26/44 (59%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E LK  F K+G +    + +D  TGRSRGF ++ F+  E  +KA
Sbjct: 14  EWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKA 57

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 16/35 (45%), Positives = 26/35 (74%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVF 148
           E+L+E F ++G+IE V++  D NTG S+GF ++ F
Sbjct: 15  EDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49

This subfamily corresponds to the RRM2 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 = 74

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 16/35 (45%), Positives = 26/35 (74%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVF 642
           E+L+E F ++G+IE V++  D NTG S+GF ++ F
Sbjct: 15  EDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49

This subfamily corresponds to the RRM2 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 = 74

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 17/60 (28%), Positives = 35/60 (58%), Gaps = 8/60 (13%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+FVG L PE  ++EI++ F Q+G ++E ++         KN+ F+  + ++   + ++N
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRN 53

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>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 = 42.0 bits (99), Expect = 3e-05
 Identities = 13/51 (25%), Positives = 29/51 (56%)

Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
           ++++ ++  D    + + F F+TF+ ES V  +      ++  K+V+VK+A
Sbjct: 25  KVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAGMLELGGKQVEVKRA 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 46.7 bits (111), Expect = 3e-05
 Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
           E+L+E FS+ GEI +  +  D   G SRGF F+ F + E   +A  E
Sbjct: 300 EKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTE 345

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|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 18/38 (47%), Positives = 24/38 (63%)

Query: 614 FSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           FSKYG++  VT+  D  T +S+G AFI+F D E   K 
Sbjct: 22  FSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKC 59

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|219320 pfam07172, GRP, Glycine rich protein family

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 23/51 (45%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 252 DKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
           + E    +   + + +G  GG GG GG GG G    G YGG GGYGGG GG
Sbjct: 30  NTEKSESENEVQDDKYG--GGGGGYGGGGGGGYGGGGYYGGGGGYGGGGGG 78

This family of proteins includes several glycine rich proteins as well as two nodulins 16 and 24. The family also contains proteins that are induced in response to various stresses. Length = 91

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 18/52 (34%), Positives = 32/52 (61%), Gaps = 2/52 (3%)

Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE-SLEK 156
           G+   +TE +L+E FS++G + +V +    + G  RGFA+I  + +E  L+K
Sbjct: 6   GLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKK 57

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

 Score = 42.4 bits (99), Expect = 3e-05
 Identities = 19/47 (40%), Positives = 30/47 (63%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
           +FVG LSPE+  ++IKA FA FG I +  +  D +  + K + F++F
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 50

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|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 42.1 bits (100), Expect = 3e-05
 Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 12/56 (21%)

Query: 602 IVDKITEE------LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            V  I  E      L EHFSK+G I N+ +  +P +      A + F  +E  +KA
Sbjct: 5   EVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPES------ALVQFSTSEEAKKA 54

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

 Score = 42.4 bits (99), Expect = 3e-05
 Identities = 19/47 (40%), Positives = 30/47 (63%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
           +FVG LSPE+  E+IK+ FA FG I +  +  D +  + K + F++F
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 50

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|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 = 41.8 bits (99), Expect = 3e-05
 Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 7/52 (13%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE-HES 237
           ++VG L   + +EE++  F+ FG I E  +  D      K + F+ F+ HE+
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEA 48

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

 Score = 43.9 bits (103), Expect = 4e-05
 Identities = 29/107 (27%), Positives = 46/107 (42%), Gaps = 8/107 (7%)

Query: 429 GTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQK-INDK 487
           GTD   +    A   ++++ ++  D+   + + F F+ F  E      +     K +N +
Sbjct: 45  GTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGR 104

Query: 488 EVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGY 534
            + V  A  +P      GG GG  G GG       GYGG G  GGG+
Sbjct: 105 HIRVNPANDRPSAPRAYGGGGGYSGGGG-------GYGGGGDGGGGF 144

Length = 144

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 41.9 bits (98), Expect = 4e-05
 Identities = 19/75 (25%), Positives = 44/75 (58%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+F+GGLS +   +++  + ++FG +++  +  D    + + F F+ F+  + V  +L+ 
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

Query: 246 PKQKINDKEVDVKKA 260
            + K++ K +D K+A
Sbjct: 61  KEHKLDGKLIDPKRA 75

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which 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. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

>gnl|CDD|219320 pfam07172, GRP, Glycine rich protein family

 Score = 42.4 bits (100), Expect = 4e-05
 Identities = 20/34 (58%), Positives = 20/34 (58%)

Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
           G  GG GG G  GG GG   GG G  GG GGGYG
Sbjct: 55  GGGGGYGGGGYYGGGGGYGGGGGGYPGGGGGGYG 88

This family of proteins includes several glycine rich proteins as well as two nodulins 16 and 24. The family also contains proteins that are induced in response to various stresses. Length = 91

>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 = 41.5 bits (98), Expect = 4e-05
 Identities = 16/49 (32%), Positives = 30/49 (61%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
           +F+  L  E  D+++   FA FGN+I  ++  DK+  Q K F F+++++
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDN 49

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|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 42.0 bits (99), Expect = 4e-05
 Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 2/47 (4%)

Query: 112 ITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           ITE +++E F K  EI +V L +D  TG  +GF  + F D ESL+ A
Sbjct: 11  ITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAA 56

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 42.0 bits (99), Expect = 4e-05
 Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 2/47 (4%)

Query: 606 ITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ITE +++E F K  EI +V L +D  TG  +GF  + F D ESL+ A
Sbjct: 11  ITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAA 56

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 45.7 bits (108), Expect = 5e-05
 Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 605 KITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           K  E +L E FSK G++ +V    D N+ RS+G A++ F D ES+ KA
Sbjct: 100 KARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKA 147

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

 Score = 41.7 bits (98), Expect = 5e-05
 Identities = 16/44 (36%), Positives = 26/44 (59%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E+L + FS    I++  + +DP TG SRG+ F+ F   E  ++A
Sbjct: 14  EDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEA 57

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|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 41.4 bits (98), Expect = 5e-05
 Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 6/44 (13%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
            +L EHFSK+G I N+ +  +P +      A + F  +E  +KA
Sbjct: 17  TKLNEHFSKFGTIVNIQVNYNPES------ALVQFSTSEEAKKA 54

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

 Score = 42.6 bits (100), Expect = 5e-05
 Identities = 16/44 (36%), Positives = 23/44 (52%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           E L  HFSK+G +       D +TGR++G  F+ FKD  +    
Sbjct: 16  ESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNAC 59

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

 Score = 42.6 bits (100), Expect = 5e-05
 Identities = 16/44 (36%), Positives = 23/44 (52%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E L  HFSK+G +       D +TGR++G  F+ FKD  +    
Sbjct: 16  ESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNAC 59

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|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 5/49 (10%)

Query: 114 EELKEHFSKYGEIENVTL-----KSDPNTGRSRGFAFIVFKDTESLEKA 157
           E LK+HF K G + +VT+        P    S G+ F+ FK  E+ +KA
Sbjct: 15  ETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKA 63

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|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 5/49 (10%)

Query: 608 EELKEHFSKYGEIENVTL-----KSDPNTGRSRGFAFIVFKDTESLEKA 651
           E LK+HF K G + +VT+        P    S G+ F+ FK  E+ +KA
Sbjct: 15  ETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKA 63

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|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 = 41.5 bits (98), Expect = 5e-05
 Identities = 13/34 (38%), Positives = 23/34 (67%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDK 220
           +FVGGL P + ++E+++ F  FG I+  ++P  K
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGK 37

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|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 = 41.4 bits (98), Expect = 6e-05
 Identities = 18/49 (36%), Positives = 27/49 (55%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
           K+FVG L     +E+++A F ++GNI E  +  DK   Q K   F+ F 
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFS 49

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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 41.6 bits (97), Expect = 6e-05
 Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 2/79 (2%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH-ESVVIDLLK 244
           K+F+GGLS E  D+ ++ HF ++G + +  +  D    + + F F+T+   E V   +  
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63

Query: 245 NPKQKINDKEVDVKKATPK 263
            P  K++ + V+ K+A  +
Sbjct: 64  RP-HKVDGRVVEPKRAVSR 81

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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 41.6 bits (97), Expect = 6e-05
 Identities = 20/78 (25%), Positives = 42/78 (53%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+F+GGLS E  +E ++ ++ Q+G + +  +  D +  + + F F+TF   + V   +  
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63

Query: 246 PKQKINDKEVDVKKATPK 263
               I+ + V+ K+A  +
Sbjct: 64  RPHTIDGRVVEPKRAVAR 81

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which 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 A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 41.3 bits (97), Expect = 6e-05
 Identities = 15/44 (34%), Positives = 27/44 (61%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           +EL+ HF + G I  V + +  ++G+ +GFAF+ F++ E    A
Sbjct: 13  DELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA 56

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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 41.3 bits (97), Expect = 6e-05
 Identities = 15/44 (34%), Positives = 27/44 (61%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +EL+ HF + G I  V + +  ++G+ +GFAF+ F++ E    A
Sbjct: 13  DELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA 56

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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 41.5 bits (98), Expect = 6e-05
 Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 2/44 (4%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           EEL E FS++G+I  V L    N   +  FAFI F+  ++  +A
Sbjct: 18  EELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARA 59

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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 41.5 bits (98), Expect = 6e-05
 Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 2/44 (4%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           EEL E FS++G+I  V L    N   +  FAFI F+  ++  +A
Sbjct: 18  EELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARA 59

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 40.6 bits (96), Expect = 6e-05
 Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 11/66 (16%)

Query: 116 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGN-HVINNKK 174
           L + FS +G +E + L       +  GFAF+ F   E+ EKA     +   N  +   + 
Sbjct: 1   LYKLFSPFGNVEKIKL-----LKKKPGFAFVEFSTEEAAEKA-----VQYLNGVLFGGRP 50

Query: 175 IEAKKA 180
           +    +
Sbjct: 51  LRVDYS 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|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 17/52 (32%), Positives = 32/52 (61%), Gaps = 7/52 (13%)

Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           G+ +++TE+ L++HF ++GEI ++T+         +  AF+ F   E+ EKA
Sbjct: 8   GLGERVTEKDLRDHFYQFGEIRSITVVP------RQQCAFVTFTTREAAEKA 53

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

 Score = 41.2 bits (97), Expect = 7e-05
 Identities = 14/50 (28%), Positives = 29/50 (58%)

Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
           +G++FV  L    K+++++  F++FG + E  +  DK   + K F ++ F
Sbjct: 2   TGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLF 51

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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 45.8 bits (108), Expect = 7e-05
 Identities = 40/144 (27%), Positives = 64/144 (44%), Gaps = 21/144 (14%)

Query: 105 HPGI-----VHKITEELKEH-----FSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESL 154
            PG      V KI  +L E      F K G I  + L  D + G++RG+AF+ F   E  
Sbjct: 54  QPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFS-GQNRGYAFVTFCGKEEA 112

Query: 155 EKASVEDVIAEGNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFG----N 210
           ++A    V    N+ I   ++        + ++FVGG+    K EEI   F++      +
Sbjct: 113 KEA----VKLLNNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVD 168

Query: 211 IIETEMPYDKSKSQRKNFCFITFE 234
           +I      DK K+  + F F+ +E
Sbjct: 169 VIVYHSAADKKKN--RGFAFVEYE 190

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. Length = 578

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 41.0 bits (96), Expect = 8e-05
 Identities = 21/53 (39%), Positives = 31/53 (58%), Gaps = 1/53 (1%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVV 239
           +FVG L P++ +E I   F Q G +I+ ++P DK     K F F+ F+HE  V
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKP-KQFAFVNFKHEVSV 55

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 44.7 bits (106), Expect = 8e-05
 Identities = 20/35 (57%), Positives = 20/35 (57%)

Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
           G  GGRGG  G GG GGR  GG GG  G G G G 
Sbjct: 5   GFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGR 39

Length = 293

>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 41.0 bits (97), Expect = 8e-05
 Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 112 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           +TE  L E FS  G + ++ +  D  T RS G+A++ F++    E+A
Sbjct: 11  VTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERA 57

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|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 41.0 bits (97), Expect = 8e-05
 Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 606 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +TE  L E FS  G + ++ +  D  T RS G+A++ F++    E+A
Sbjct: 11  VTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERA 57

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|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 41.1 bits (97), Expect = 9e-05
 Identities = 17/44 (38%), Positives = 28/44 (63%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           E+L+  FS++G+I++  +  D  TG S  +AFI F+  E  E+A
Sbjct: 18  EDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

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|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 41.1 bits (97), Expect = 9e-05
 Identities = 17/44 (38%), Positives = 28/44 (63%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E+L+  FS++G+I++  +  D  TG S  +AFI F+  E  E+A
Sbjct: 18  EDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

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|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional

 Score = 44.3 bits (105), Expect = 9e-05
 Identities = 22/56 (39%), Positives = 34/56 (60%), Gaps = 6/56 (10%)

Query: 597 VSHPGIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           VS+  +  K TE ++KE FS  G+IE V ++S+    RS+  A++ FKD +  E A
Sbjct: 9   VSN--VSLKATERDIKEFFSFSGDIEYVEMQSE--NERSQ-IAYVTFKDPQGAETA 59

Length = 260

>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 = 1e-04
 Identities = 15/75 (20%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMP---YDKSKSQRKNFCFITFEHESVVIDL 242
           +I+V  L  ++ +++++  F++FG +    +P    +K       F F+TF+  S   + 
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 243 LKNPKQKINDKEVDV 257
           L+    ++  +++ V
Sbjct: 62  LQLNGTELGGRKISV 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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 4/62 (6%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVV---IDLL 243
           +FVG L   + +E +   F Q G +   ++P D    + K+F F+TF+HE  V   I LL
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDP-NGKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 244 KN 245
             
Sbjct: 63  NG 64

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 40.2 bits (95), Expect = 1e-04
 Identities = 14/48 (29%), Positives = 27/48 (56%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
           +FVGGLSP + + +++  F++FG + + E+   K     + F +I   
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLR 49

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 39.8 bits (94), Expect = 1e-04
 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 5/42 (11%)

Query: 610 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           L + FS +G +E + L       +  GFAF+ F   E+ EKA
Sbjct: 1   LYKLFSPFGNVEKIKL-----LKKKPGFAFVEFSTEEAAEKA 37

(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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 20/41 (48%), Positives = 22/41 (53%)

Query: 270 RGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLF 310
            GGRGG  G G   GR  GG G  GG GGG G ++  P  F
Sbjct: 24  GGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGKVIVVPHRF 64

Length = 293

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 19/44 (43%), Positives = 27/44 (61%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           EEL+ HFS  G I  VT+  D  +G  +G+A+I F   +S+E A
Sbjct: 14  EELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAA 57

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 19/44 (43%), Positives = 27/44 (61%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           EEL+ HFS  G I  VT+  D  +G  +G+A+I F   +S+E A
Sbjct: 14  EELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAA 57

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 16/58 (27%), Positives = 25/58 (43%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK 244
           +FVG L  +   E++ AHF   G      +  DK   + K   F+ F+    +   LK
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK 60

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|219320 pfam07172, GRP, Glycine rich protein family

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 22/50 (44%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 486 DKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
           + E    +   + + +G  GG GG GG GG G    G YGG GGYGGG G
Sbjct: 30  NTEKSESENEVQDDKYG--GGGGGYGGGGGGGYGGGGYYGGGGGYGGGGG 77

This family of proteins includes several glycine rich proteins as well as two nodulins 16 and 24. The family also contains proteins that are induced in response to various stresses. Length = 91

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
           IFVG LSP++  EE+   F++ G I+  E+   K  +    F FI FE E 
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKIL--EVNLIKRANHTNAFAFIKFEREQ 54

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 43.6 bits (103), Expect = 2e-04
 Identities = 20/34 (58%), Positives = 20/34 (58%)

Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
           G  GGRGG  G GG GGR  GG GG  G G G G
Sbjct: 5   GFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRG 38

Length = 293

>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional

 Score = 43.1 bits (102), Expect = 2e-04
 Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 3/44 (6%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
            ++KE FS  G+IE V ++S+    RS+  A++ FKD +  E A
Sbjct: 19  RDIKEFFSFSGDIEYVEMQSE--NERSQ-IAYVTFKDPQGAETA 59

Length = 260

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 18/73 (24%)

Query: 115 ELKEHFSKYGEIENVTLKSDP-----------------NTGRSRGFAFIVFKDTESLEKA 157
           +LK+ F ++G IE+V  +S P                 +  +    A++VFK+ ES EKA
Sbjct: 16  DLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNAYVVFKEEESAEKA 75

Query: 158 SVED-VIAEGNHV 169
              +    EG+H+
Sbjct: 76  LKLNGTEFEGHHI 88

This subfamily corresponds to the RRM1 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 = 91

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 12/64 (18%)

Query: 604 DKIT-EELKEH----FSKYGEI-ENVTLKSDPNTGRSRGFAFIVFKDTESLEKA--SVED 655
           +KI  +ELK      FS++G + + V  K+     + RG AF+VFKD ES   A  +++ 
Sbjct: 9   EKIKKDELKRSLYALFSQFGPVLDIVASKTL----KMRGQAFVVFKDVESATNALRALQG 64

Query: 656 VYFY 659
             FY
Sbjct: 65  FPFY 68

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 9/72 (12%)

Query: 112 ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEG-NHVI 170
           +   + EHFSKYG +  V +  D    R R +AF+ F + +  + A     +A+G   ++
Sbjct: 19  LEAAVTEHFSKYGTLVFVKVLRD---WRQRPYAFVQFTNDDDAKNA-----LAKGQGTIL 70

Query: 171 NNKKIEAKKAKA 182
           + + I  ++AK 
Sbjct: 71  DGRHIRCERAKV 82

This subfamily corresponds to the RRM1 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 = 86

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 14/44 (31%), Positives = 27/44 (61%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           ++L+E F+ +GEI+++ +  D  T  S+G A++ F    S  +A
Sbjct: 17  DDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARA 60

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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 14/44 (31%), Positives = 27/44 (61%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ++L+E F+ +GEI+++ +  D  T  S+G A++ F    S  +A
Sbjct: 17  DDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARA 60

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|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 15/40 (37%), Positives = 23/40 (57%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
           ++++ HF  +GEIE   LK DP TG+S G   + F+    
Sbjct: 13  KQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPL 52

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 15/40 (37%), Positives = 23/40 (57%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
           ++++ HF  +GEIE   LK DP TG+S G   + F+    
Sbjct: 13  KQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPL 52

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 13/48 (27%), Positives = 28/48 (58%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
           K+FVG +   + ++E++  F + GN++E  +  DK    ++  CF+ +
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKY 48

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|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 = 16/46 (34%), Positives = 25/46 (54%), Gaps = 3/46 (6%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 158
           +EEL + F KYG I  + + +   T   RG AF+V++D    + A 
Sbjct: 16  SEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNAC 58

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|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 = 16/46 (34%), Positives = 25/46 (54%), Gaps = 3/46 (6%)

Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 652
           +EEL + F KYG I  + + +   T   RG AF+V++D    + A 
Sbjct: 16  SEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNAC 58

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

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 15/48 (31%), Positives = 24/48 (50%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
           ++V  L      E +KA F+++G ++   +P  K     K F FI FE
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFE 49

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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 9/75 (12%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETE-MPYDKSKSQRKNFCFITFE-HESVVIDLLK 244
           ++V  L  +M DE++K  F ++G I   + M  D+ KS  K F F+ FE HE+      +
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKS--KGFGFVNFENHEAA-----Q 56

Query: 245 NPKQKINDKEVDVKK 259
              +++N KEV+ KK
Sbjct: 57  KAVEELNGKEVNGKK 71

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

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 4/68 (5%)

Query: 189 VGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQ 248
           V GLS    + +++  F+++G I + ++ YD+   + + F F+ FE     ++  K  K+
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFES----VEDAKEAKE 59

Query: 249 KINDKEVD 256
           ++N  E+D
Sbjct: 60  RLNGMEID 67

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

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 4/71 (5%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            +FVG LS  + DE +KA F +FG ++   +  D+   + + F ++ FE         K 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDA----KK 56

Query: 246 PKQKINDKEVD 256
             + ++ KE+D
Sbjct: 57  AIEAMDGKELD 67

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|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 16/79 (20%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  ++TE+ L++HF ++GEI ++T+         +  AF+ F   E+ EKA      AE
Sbjct: 8   GLGERVTEKDLRDHFYQFGEIRSITVVP------RQQCAFVTFTTREAAEKA------AE 55

Query: 166 GNH---VINNKKIEAKKAK 181
                 +IN ++++ K  +
Sbjct: 56  RLFNKLIINGRRLKLKWGR 74

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 43.2 bits (102), Expect = 3e-04
 Identities = 21/35 (60%), Positives = 21/35 (60%)

Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
           G  GGRGG G  GGRGG    G GG GG  GG GG
Sbjct: 17  GGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGG 51

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 42.8 bits (101), Expect = 3e-04
 Identities = 18/33 (54%), Positives = 18/33 (54%)

Query: 270 RGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
             G G  GGRGG  G   GG  G GG GGG GG
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGG 33

Length = 293

>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 12/68 (17%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRG-FAFIVFKDTESLEKASVEDVIAEGNHVINN 172
           E+L ++FS +G + NV +  D      +G +A + F   E ++K     V++E  H +N 
Sbjct: 17  EQLMDYFSAFGPVMNVIMDKD------KGVYAIVEFDSKEGVDK-----VLSEPQHTLNG 65

Query: 173 KKIEAKKA 180
            ++  +  
Sbjct: 66  HRLRVRPR 73

This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). . Length = 74

>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX) proteins

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 23/53 (43%), Positives = 26/53 (49%), Gaps = 7/53 (13%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVV 239
           +FVGGL     +E I+  F Q G II   M    SK   KNFC I F  E  V
Sbjct: 9   VFVGGLPENATEEIIREVFEQCGEIIAIRM----SK---KNFCHIRFAEEFAV 54

This subgroup corresponds to the conserved RNA recognition motif (RRM) in ECTO-NOX proteins (also termed ENOX), comprising a family of plant and animal NAD(P)H oxidases exhibiting both, oxidative and protein disulfide isomerase-like, activities. They are growth-related and drive cell enlargement, and may play roles in aging and neurodegenerative diseases. ENOX proteins function as terminal oxidases of plasma membrane electron transport (PMET) through catalyzing electron transport from plasma membrane quinones to extracellular oxygen, forming water as a product. They are also hydroquinone oxidases that oxidize externally supplied NADH, hence NOX. ENOX proteins harbor a di-copper center that lack flavin. ENOX proteins display protein disulfide interchange activity that is also possessed by protein disulfide isomerase. In contrast to the classic protein disulfide isomerases, ENOX proteins lack the double CXXC motif. This family includes two ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed candidate growth-related and time keeping constitutive hydroquinone [NADH] oxidase (cCNOX), or cell proliferation-inducing gene 38 protein, or Constitutive Ecto-NOX (cNOX), is the constitutively expressed cell surface NADH (ubiquinone) oxidase that is ubiquitous and refractory to drugs. ENOX2, also termed APK1 antigen, or cytosolic ovarian carcinoma antigen 1, or tumor-associated hydroquinone oxidase (tNOX), is a cancer-specific variant of ENOX1 and plays a key role in cell proliferation and tumor progression. In contrast to ENOX1, ENOX2 is drug-responsive and harbors a drug binding site to which the cancer-specific S-peptide tagged pan-ENOX2 recombinant (scFv) is directed. Moreover, ENOX2 is specifically inhibited by a variety of quinone site inhibitors that have anticancer activity and is unique to the surface of cancer cells. ENOX proteins contain many functional motifs. Length = 84

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

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 16/44 (36%), Positives = 27/44 (61%), Gaps = 1/44 (2%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           ++L+E F + GE+ +V +  D + GRS+GF  + F   E  +KA
Sbjct: 14  DDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKA 56

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

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 16/44 (36%), Positives = 27/44 (61%), Gaps = 1/44 (2%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ++L+E F + GE+ +V +  D + GRS+GF  + F   E  +KA
Sbjct: 14  DDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKA 56

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

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 13/46 (28%), Positives = 22/46 (47%)

Query: 192 LSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
           LS +  +++++  F  FG I    +  DK   Q + F F+TF    
Sbjct: 7   LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTRE 52

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|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 6/55 (10%)

Query: 601 GIVDKITEE-LKEHFSKYG--EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 652
           G+    TEE + +  S      I++V L  D  TG SRGFAF+ F    SLE A+
Sbjct: 9   GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEF---PSLEDAT 60

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It 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. All family members 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 = 84

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 15/44 (34%), Positives = 27/44 (61%), Gaps = 1/44 (2%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE-SLEK 650
            +L+E FS++G + +V +    + G  RGFA+I  + +E  L+K
Sbjct: 14  SDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKK 57

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 42.8 bits (101), Expect = 4e-04
 Identities = 17/36 (47%), Positives = 17/36 (47%)

Query: 267 FGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
               G  GGRGG  G GG    G GG GG  GG  G
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRG 36

Length = 293

>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 = 20/71 (28%), Positives = 32/71 (45%), Gaps = 12/71 (16%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+FVG L      EE++A F ++G + E ++         KN+ F+  E E    D +K 
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDV--------VKNYGFVHMEEEEDAEDAIKA 52

Query: 246 PKQKINDKEVD 256
               +N  E  
Sbjct: 53  ----LNGYEFM 59

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

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 14/49 (28%), Positives = 27/49 (55%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
           +I+V  + P++ +++IK+ F  FG I    +  D    + K + FI +E
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYE 50

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|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 = 19/63 (30%), Positives = 31/63 (49%), Gaps = 12/63 (19%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           E+L+E FSKYG+I  ++L         +G+ F+ F + E    A    V  E    I  +
Sbjct: 16  EDLEEIFSKYGKILGISLH--------KGYGFVQFDNEEDARAA----VAGENGREIAGQ 63

Query: 174 KIE 176
           K++
Sbjct: 64  KLD 66

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|180777 PRK06958, PRK06958, single-stranded DNA-binding protein; Provisional

 Score = 41.7 bits (98), Expect = 4e-04
 Identities = 22/32 (68%), Positives = 22/32 (68%), Gaps = 1/32 (3%)

Query: 271 GGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
           GGRGG GG GG GG   G  GG GG GGGYGG
Sbjct: 109 GGRGGSGG-GGGGGDEGGYGGGGGGGGGGYGG 139

Length = 182

>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins

 Score = 40.0 bits (94), Expect = 4e-04
 Identities = 12/39 (30%), Positives = 19/39 (48%)

Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
            +K +FS +GEI  +   +DPNT    G   I +  +  
Sbjct: 18  IIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPG 56

This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and activating transcription. scSet1p is closely related to the SET domain proteins of multicellular organisms, which are implicated in diverse aspects of cell morphology, growth control, and chromatin-mediated transcriptional silencing. scSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 110

>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins

 Score = 40.0 bits (94), Expect = 4e-04
 Identities = 12/39 (30%), Positives = 19/39 (48%)

Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
            +K +FS +GEI  +   +DPNT    G   I +  +  
Sbjct: 18  IIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPG 56

This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and activating transcription. scSet1p is closely related to the SET domain proteins of multicellular organisms, which are implicated in diverse aspects of cell morphology, growth control, and chromatin-mediated transcriptional silencing. scSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 110

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 39.6 bits (92), Expect = 4e-04
 Identities = 19/48 (39%), Positives = 28/48 (58%)

Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           D  +E+L+  F +YG I +V +  D  T R RGFA++ F+D    E A
Sbjct: 11  DTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDA 58

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|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 39.3 bits (91), Expect = 4e-04
 Identities = 17/43 (39%), Positives = 28/43 (65%)

Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           +L+E FS  G++ +V + SD N+ RS+G A++ F D  S+  A
Sbjct: 17  DLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLA 59

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor 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. 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|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 39.3 bits (91), Expect = 4e-04
 Identities = 17/43 (39%), Positives = 28/43 (65%)

Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +L+E FS  G++ +V + SD N+ RS+G A++ F D  S+  A
Sbjct: 17  DLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLA 59

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor 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. 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|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 = 39.0 bits (91), Expect = 4e-04
 Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 10/77 (12%)

Query: 187 IFVGGLSPE-MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           +FV G  P   ++E+I+  F  FG ++  ++        RK F F+ FE        L+ 
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSEDATKALEA 53

Query: 246 -PKQKINDKEVDVKKAT 261
               +I+   + V+   
Sbjct: 54  LHGSRIDGSVLTVEFVK 70

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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 18/45 (40%), Positives = 33/45 (73%), Gaps = 1/45 (2%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
            +EL++ FSK GEI +V L  +   G+S+G+A++ F++ ES+++A
Sbjct: 13  EDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEA 56

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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 18/45 (40%), Positives = 33/45 (73%), Gaps = 1/45 (2%)

Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            +EL++ FSK GEI +V L  +   G+S+G+A++ F++ ES+++A
Sbjct: 13  EDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEA 56

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|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 42.7 bits (100), Expect = 5e-04
 Identities = 19/85 (22%), Positives = 47/85 (55%), Gaps = 2/85 (2%)

Query: 152 ESLEKASVEDVIAEGNHVINNKKIEAKKAKAKS--GKIFVGGLSPEMKDEEIKAHFAQFG 209
           +S+++  ++   A     + N++ + ++ +A +   +++VG +S E++++ I+  F  FG
Sbjct: 73  QSIKQVLLKQTKAHQQQQLENQQRQQQRQQALAIMCRVYVGSISFELREDTIRRAFDPFG 132

Query: 210 NIIETEMPYDKSKSQRKNFCFITFE 234
            I    M +D +  + K F F+ +E
Sbjct: 133 PIKSINMSWDPATGKHKGFAFVEYE 157

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 42.0 bits (99), Expect = 5e-04
 Identities = 22/35 (62%), Positives = 22/35 (62%), Gaps = 2/35 (5%)

Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
           G RGG G  GGRGG  GR  G  GG GG GGG GG
Sbjct: 20  GGRGGGGRGGGRGGGRGR--GRGGGGGGRGGGGGG 52

Length = 293

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 39.2 bits (91), Expect = 5e-04
 Identities = 18/45 (40%), Positives = 27/45 (60%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           +E+L+  F +YG I +V +  D  T R RGFA++ F+D    E A
Sbjct: 14  SEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDA 58

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 39.0 bits (91), Expect = 5e-04
 Identities = 20/80 (25%), Positives = 46/80 (57%), Gaps = 4/80 (5%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           +IFVGG+  +  + +++  F+Q+G + E ++  D++    K + F+TFE +     +L+ 
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRA-GVSKGYGFVTFETQEDAQKILQE 62

Query: 246 PKQKIN--DKEVDVKKATPK 263
              ++   DK++++ +A  K
Sbjct: 63  AN-RLCFRDKKLNIGQAIRK 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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 38.5 bits (89), Expect = 6e-04
 Identities = 17/51 (33%), Positives = 29/51 (56%)

Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
           EI   E+P D   ++R+ FCF+T+  E  V  LL++   +I   + ++K A
Sbjct: 25  EIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLESRYHQIGSGKCEIKVA 75

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), 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. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 38.7 bits (90), Expect = 6e-04
 Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
            +LK+ F +YG++   T+      G+  GFAF+  K  ++ E A
Sbjct: 16  VKLKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIA 58

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

 Score = 38.7 bits (90), Expect = 6e-04
 Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            +LK+ F +YG++   T+      G+  GFAF+  K  ++ E A
Sbjct: 16  VKLKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIA 58

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

 Score = 38.9 bits (90), Expect = 6e-04
 Identities = 20/44 (45%), Positives = 26/44 (59%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           EELK  F   GEIE+  L  D  TG+S G+ F+ + D +  EKA
Sbjct: 19  EELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62

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

 Score = 38.9 bits (90), Expect = 6e-04
 Identities = 20/44 (45%), Positives = 26/44 (59%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           EELK  F   GEIE+  L  D  TG+S G+ F+ + D +  EKA
Sbjct: 19  EELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62

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

 Score = 38.6 bits (90), Expect = 6e-04
 Identities = 15/47 (31%), Positives = 27/47 (57%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
           IFVG LSPE+ D  + A F+ F +  +  + +D    + + + F++F
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSF 48

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|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 = 38.4 bits (90), Expect = 7e-04
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESV---VIDL 242
           KIF+GGL   + ++++K     FG +    +  D +    K + F  +   SV    I  
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 243 LKNPKQKINDKEVDVKKA 260
           L     ++ DK++ V++A
Sbjct: 62  LNG--MQLGDKKLTVQRA 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|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 38.3 bits (90), Expect = 7e-04
 Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
           ++V    P     +I+  F Q+G I+    P  +    R+ FC++ F    
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRR-FCYVQFTSPE 52

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|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 7/59 (11%)

Query: 594 NKMVSHPGIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
              V   G+ + +TE+ L  HFS+YG + +V +       R RG A + F   E+ + A
Sbjct: 7   TNCVWLDGLDESVTEQYLTRHFSRYGPVVHVVID------RQRGQALVFFDKVEAAQAA 59

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 38.5 bits (89), Expect = 7e-04
 Identities = 19/44 (43%), Positives = 26/44 (59%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           E+L+  F +YG I +V +  D  T R RGFA+I F+D    E A
Sbjct: 15  EDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDA 58

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|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 38.5 bits (89), Expect = 7e-04
 Identities = 19/44 (43%), Positives = 26/44 (59%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E+L+  F +YG I +V +  D  T R RGFA+I F+D    E A
Sbjct: 15  EDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDA 58

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|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 = 38.3 bits (89), Expect = 7e-04
 Identities = 16/49 (32%), Positives = 29/49 (59%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
           +F+  L  E  D E+   F  FGN+I  ++  D++ +Q K F F++F++
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDN 55

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

 Score = 38.5 bits (90), Expect = 7e-04
 Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 115 ELKEHFSKYGEIENVTLKSDPN-TGRSRGFAFIVFKDTESLEKA 157
           EL+E FS +GE++ V L      TG  RGF F+ F   +  ++A
Sbjct: 16  ELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRA 59

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

 Score = 38.5 bits (90), Expect = 7e-04
 Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 609 ELKEHFSKYGEIENVTLKSDPN-TGRSRGFAFIVFKDTESLEKA 651
           EL+E FS +GE++ V L      TG  RGF F+ F   +  ++A
Sbjct: 16  ELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRA 59

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|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 38.7 bits (91), Expect = 8e-04
 Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 3/52 (5%)

Query: 603 VDKITEELKEHFSKYGEIENVTL---KSDPNTGRSRGFAFIVFKDTESLEKA 651
            ++I E++KE   KYG++ +V +   +++       G  F+ F D E  +KA
Sbjct: 21  YEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKA 72

This subfamily corresponds to the RRM3 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 = 89

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

 Score = 38.3 bits (89), Expect = 8e-04
 Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 3/58 (5%)

Query: 112 ITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA--SVEDVIAEG 166
           +TE EL++ F  YG I    L  D +TG  RG AF+ +   E  + A  S+   I  G
Sbjct: 12  LTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTIPPG 69

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|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins

 Score = 38.8 bits (91), Expect = 8e-04
 Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 16/61 (26%)

Query: 113 TEE-LKEHFSKYGEIENVTLKSDPNTGRS-------------RGF--AFIVFKDTESLEK 156
           TEE LK  FS+ G++E+V L+  P    S             +GF  A++VFK   SL +
Sbjct: 13  TEESLKRLFSRCGKVESVELQEKPGPAESEDLTSKFFPPKPIKGFKVAYVVFKKPSSLSR 72

Query: 157 A 157
           A
Sbjct: 73  A 73

This subfamily corresponds to the RRM of Rrp7A, also termed gastric cancer antigen Zg14, a homolog of yeast ribosomal RNA-processing protein 7 (Rrp7p), and mainly found in Metazoa. Rrp7p is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. In contrast, the cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal Rrp7 domain. . Length = 102

>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins

 Score = 38.8 bits (91), Expect = 8e-04
 Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 16/61 (26%)

Query: 607 TEE-LKEHFSKYGEIENVTLKSDPNTGRS-------------RGF--AFIVFKDTESLEK 650
           TEE LK  FS+ G++E+V L+  P    S             +GF  A++VFK   SL +
Sbjct: 13  TEESLKRLFSRCGKVESVELQEKPGPAESEDLTSKFFPPKPIKGFKVAYVVFKKPSSLSR 72

Query: 651 A 651
           A
Sbjct: 73  A 73

This subfamily corresponds to the RRM of Rrp7A, also termed gastric cancer antigen Zg14, a homolog of yeast ribosomal RNA-processing protein 7 (Rrp7p), and mainly found in Metazoa. Rrp7p is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. In contrast, the cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal Rrp7 domain. . Length = 102

>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 38.0 bits (89), Expect = 9e-04
 Identities = 19/52 (36%), Positives = 32/52 (61%), Gaps = 2/52 (3%)

Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           GI    TE EL++ FS++G +++V + +D   G S+G+ F+ F+  E  EK 
Sbjct: 9   GIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKI 59

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

 Score = 38.3 bits (90), Expect = 9e-04
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 110 HKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
              TEE + E FS+ G+I+ + +  D  T    GF F+ +   E  E A
Sbjct: 8   FYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENA 56

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

 Score = 39.6 bits (92), Expect = 0.001
 Identities = 16/45 (35%), Positives = 26/45 (57%)

Query: 116 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
           L++ F+ +G++ +  +  D  TGRSRGF F+ F D  +   A  E
Sbjct: 51  LRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Length = 144

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

 Score = 39.6 bits (92), Expect = 0.001
 Identities = 16/45 (35%), Positives = 26/45 (57%)

Query: 610 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           L++ F+ +G++ +  +  D  TGRSRGF F+ F D  +   A  E
Sbjct: 51  LRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Length = 144

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

 Score = 41.3 bits (97), Expect = 0.001
 Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 610 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           L + FSK+G I +  + +D N G+SRG+ F+ F+  ES + A  +
Sbjct: 105 LFDTFSKFGNILSCKVATDEN-GKSRGYGFVHFEKEESAKAAIQK 148

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 12/47 (25%), Positives = 24/47 (51%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
           ++VG L   + +++++  F  FG I   ++  D    + K + FI F
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQF 47

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 14/54 (25%), Positives = 31/54 (57%), Gaps = 3/54 (5%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKS---KSQRKNFCFITFEHE 236
           ++++G L   + +  +   F+++G I + +  + KS   K Q + +CF+TFE +
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETK 54

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|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 14/51 (27%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE 236
           ++ V  L   +K+++++  F  FG I + ++ Y K    RK F F+ ++ E
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRK-FGFVGYKTE 51

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 21/34 (61%), Positives = 21/34 (61%)

Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
           G RGG G  GGRGG  GR  GG GG  G GGG G
Sbjct: 20  GGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGG 53

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 20/34 (58%), Positives = 20/34 (58%)

Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
           G  GGRGG G  GGRGG    G GG GG  GG G
Sbjct: 17  GGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGG 50

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 17/32 (53%), Positives = 17/32 (53%)

Query: 504 RGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
             G G  GGRGG  G   GG  G GG GGG G
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRG 32

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 16/35 (45%), Positives = 16/35 (45%)

Query: 501 FGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
               G  GGRGG  G GG    G GG GG  GG  
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGR 35

Length = 293

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 38.4 bits (90), Expect = 0.001
 Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 17/62 (27%)

Query: 609 ELKEHFSKYGEIENVTLKSDP-----------------NTGRSRGFAFIVFKDTESLEKA 651
           +LK+ F ++G IE+V  +S P                 +  +    A++VFK+ ES EKA
Sbjct: 16  DLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNAYVVFKEEESAEKA 75

Query: 652 SV 653
             
Sbjct: 76  LK 77

This subfamily corresponds to the RRM1 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 = 91

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 10/53 (18%)

Query: 111 KIT-EELKEH----FSKYGEI-ENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           KI  +ELK      FS++G + + V  K+     + RG AF+VFKD ES   A
Sbjct: 10  KIKKDELKRSLYALFSQFGPVLDIVASKTL----KMRGQAFVVFKDVESATNA 58

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 38.3 bits (90), Expect = 0.001
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 3/49 (6%)

Query: 112 ITEELKEHFSKYGEIENVTL---KSDPNTGRSRGFAFIVFKDTESLEKA 157
           I E++KE   KYG++ +V +   +++       G  F+ F D E  +KA
Sbjct: 24  ILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKA 72

This subfamily corresponds to the RRM3 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 = 89

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

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 607 TEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           TEE + E FS+ G+I+ + +  D  T    GF F+ +   E  E A
Sbjct: 11  TEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENA 56

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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 5/44 (11%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
            EL++ F KYG + +V +  +P      GFAF+ F+D    E A
Sbjct: 14  RELEDEFEKYGPLRSVWVARNPP-----GFAFVEFEDPRDAEDA 52

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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 5/44 (11%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            EL++ F KYG + +V +  +P      GFAF+ F+D    E A
Sbjct: 14  RELEDEFEKYGPLRSVWVARNPP-----GFAFVEFEDPRDAEDA 52

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|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 38.0 bits (88), Expect = 0.001
 Identities = 25/82 (30%), Positives = 36/82 (43%), Gaps = 24/82 (29%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           +EL++ FS+YG I    +  D  TG SRG  FI F                       +K
Sbjct: 15  KELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRF-----------------------DK 51

Query: 174 KIEAKKA-KAKSGKIFVGGLSP 194
           +IEA++A K  +G+   G   P
Sbjct: 52  RIEAEEAIKGLNGQKPEGASEP 73

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 23/78 (29%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           E+L+E FS+ G I+   +  D  + + RGF ++ F        A  ED            
Sbjct: 14  EQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTF--------ALEED------------ 53

Query: 174 KIEAKKAKAKSGKIFVGG 191
              AK+A  +  K   GG
Sbjct: 54  ---AKRALEEKKKTKFGG 68

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 4/53 (7%)

Query: 105 HPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           H  +     E+L+E F + GE++ V +  D  +GRS G A +VF+  E  E+A
Sbjct: 9   HYDV---TEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERA 57

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 4/53 (7%)

Query: 599 HPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           H  +     E+L+E F + GE++ V +  D  +GRS G A +VF+  E  E+A
Sbjct: 9   HYDV---TEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERA 57

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

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 6/49 (12%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
           ++FVG L  ++ +EE K  F+++G + E  +       + K F FI  +
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFLN------KEKGFGFIRLD 45

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|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 593 KNKMVSHPGIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
             + V+   + D I E  LK+   KYGE+E V +   P T +  G A +VF   +S ++ 
Sbjct: 1   PPREVTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRC 60

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            + V GL  +  ++++K +F+ FG ++  ++  D    Q K F F+ F      + +L  
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

Query: 246 PKQKINDKEVDVKKATPK 263
            +  I+ +  DVK    K
Sbjct: 61  -RHMIDGRWCDVKIPNSK 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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           +FV  L+ +  + +++  F ++G I    +  DK   + + + FI FEHE  +    K  
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 247 K-QKINDKE--VDVKKA 260
             +KI+ +   VDV++ 
Sbjct: 64  DGKKIDGRRVLVDVERG 80

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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 15/52 (28%), Positives = 27/52 (51%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESV 238
           I++G L     ++E+K +F+QFG +    +   K     K++ FI F +  V
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEV 53

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|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 15/51 (29%), Positives = 28/51 (54%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
           +FVG LS +  +E ++  F+++G+I    +  D      K + F+ +EHE 
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHER 56

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

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 12/40 (30%), Positives = 27/40 (67%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
           + +++ FS +G I+++ +  DP T + +GFAF+ ++  E+
Sbjct: 15  DTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEA 54

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

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 12/40 (30%), Positives = 27/40 (67%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
           + +++ FS +G I+++ +  DP T + +GFAF+ ++  E+
Sbjct: 15  DTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEA 54

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|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 = 37.2 bits (87), Expect = 0.002
 Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE 646
           G+ + ++E+ +KE    +G+++   L  D  TG S+G+AF  + D  
Sbjct: 7   GLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPS 53

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|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 6/47 (12%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
           ++VGGL   + +++++ HF QFG I    +        R+   F+TF
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITV------VPRQQCAFVTF 44

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 21/36 (58%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 268 GVRGGRGGRGGRGGRGG-RMAGGYGGYGGYGGGYGG 302
           G  GG GG  G GGRGG R  G   G GG GGG GG
Sbjct: 13  GRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGG 48

Length = 293

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

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 13/44 (29%), Positives = 21/44 (47%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
             L   FS +    +  +  D  +GRSRG+ F+ F+  +  E A
Sbjct: 14  ATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENA 57

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

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 13/44 (29%), Positives = 21/44 (47%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
             L   FS +    +  +  D  +GRSRG+ F+ F+  +  E A
Sbjct: 14  ATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENA 57

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|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 37.6 bits (87), Expect = 0.002
 Identities = 18/44 (40%), Positives = 24/44 (54%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +EL++ FS+YG I    +  D  TG SRG  FI F      E+A
Sbjct: 15  KELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEA 58

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 6/47 (12%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
           EE KE FSKYGE+  V L  +      +GF FI      + EKA  E
Sbjct: 16  EEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAE 56

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 6/47 (12%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           EE KE FSKYGE+  V L  +      +GF FI      + EKA  E
Sbjct: 16  EEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAE 56

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|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 19/48 (39%), Positives = 28/48 (58%)

Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           D   +EL   F K G I ++ L  DP TG +RG+AF+ F   E+ ++A
Sbjct: 12  DLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEA 59

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

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 14/49 (28%), Positives = 25/49 (51%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
           ++V GL   M  +E++A F+ +G II + +  D      +   FI F+ 
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDK 51

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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 37.6 bits (87), Expect = 0.002
 Identities = 19/48 (39%), Positives = 29/48 (60%)

Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           D   +EL   F K G I ++ L  DP +G++RG+AFI F   E+ ++A
Sbjct: 12  DLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEA 59

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R 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; it binds RNA through its RRM domains. . Length = 79

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 13/44 (29%), Positives = 25/44 (56%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
             +   F++ GE+ +V +  +  TG+S G+ F+ F   E+ E+A
Sbjct: 14  AYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQA 57

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|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 13/44 (29%), Positives = 25/44 (56%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
             +   F++ GE+ +V +  +  TG+S G+ F+ F   E+ E+A
Sbjct: 14  AYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQA 57

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|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 12/50 (24%), Positives = 25/50 (50%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE 236
           ++VG L  ++ +E +   F Q G ++   +P D+     + + F+ F  E
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSE 50

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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 37.0 bits (85), Expect = 0.003
 Identities = 16/52 (30%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           G+  + TEE L+ ++ ++G++ +  +  DP + RSRGF F+ F     ++ A
Sbjct: 9   GLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAA 60

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which 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 A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 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|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 19/47 (40%), Positives = 27/47 (57%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
           E+L++ FSKYG +  V L  D  T + +GFAF+ +   E   KA  E
Sbjct: 17  EDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

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

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 19/47 (40%), Positives = 27/47 (57%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           E+L++ FSKYG +  V L  D  T + +GFAF+ +   E   KA  E
Sbjct: 17  EDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

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

 Score = 36.8 bits (85), Expect = 0.003
 Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 606 ITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +TE EL++ F  YG I    L  D +TG  RG AF+ +   E  + A
Sbjct: 12  LTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAA 58

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|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 36.5 bits (84), Expect = 0.003
 Identities = 18/44 (40%), Positives = 27/44 (61%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           +EL   F K G I ++ L  DP TG +RG+AF+ F   E+ ++A
Sbjct: 16  DELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEA 59

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

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 27/82 (32%), Positives = 35/82 (42%), Gaps = 24/82 (29%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           +EL+  FS YG I    +  D  TG SRG  FI F                       +K
Sbjct: 15  QELEALFSPYGRIITSRILCDNVTGLSRGVGFIRF-----------------------DK 51

Query: 174 KIEAKKA-KAKSGKIFVGGLSP 194
           +IEA++A KA +G I  G   P
Sbjct: 52  RIEAERAIKALNGTIPPGATEP 73

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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 18/44 (40%), Positives = 28/44 (63%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           +EL   F K G I ++ L  DP +G++RG+AFI F   E+ ++A
Sbjct: 16  DELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEA 59

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R 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; it binds RNA through its RRM domains. . Length = 79

>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 2/48 (4%)

Query: 108 IVHK-ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
           +V K +T+E L   F     +E   LK DP TG+S+GFA++ + +  S
Sbjct: 6   VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPAS 53

This subfamily corresponds to the RRM3 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 = 75

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 16/68 (23%)

Query: 110 HKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH 168
           + +TEE LK+ FS +G I N++++ + N G      F+ F+  ES ++A     IAE   
Sbjct: 12  YGLTEEILKKAFSPFGNIINISMEKEKNCG------FVTFEKMESADRA-----IAE--- 57

Query: 169 VINNKKIE 176
            +N   ++
Sbjct: 58  -LNGTTVQ 64

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 14/71 (19%)

Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGN-HVIN 171
            E+L+E FS+YGE+E V    D        +AF+ F++ +   KA     + E N   + 
Sbjct: 15  EEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKA-----MEEMNGKELE 61

Query: 172 NKKIEAKKAKA 182
              IE   AK 
Sbjct: 62  GSPIEVSLAKP 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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 2/51 (3%)

Query: 110 HKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASV 159
           H ++E EL+  F KYG IE V +K  P  G+   +AF+ F++ +   +A V
Sbjct: 18  HNVSEVELRRAFDKYGIIEEVVIKR-PARGQGGAYAFLKFQNLDMAHRAKV 67

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 85

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

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 3/54 (5%)

Query: 601 GIVDKITEE--LKEHFSKYGEI-ENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           G +D   +E  L + FS +G I +   +  DP+TG S+GFAFI +   E+ + A
Sbjct: 7   GNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA 60

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 39.9 bits (93), Expect = 0.004
 Identities = 18/44 (40%), Positives = 26/44 (59%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           EE++  F+  GEIE+  L  D  TG+S G+ F+ +   E  EKA
Sbjct: 18  EEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61

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|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 = 36.1 bits (84), Expect = 0.004
 Identities = 12/59 (20%), Positives = 28/59 (47%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           +FVG +  +  +E++   F++ G ++   +  D+   + K + F  FE        ++N
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRN 59

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

 Score = 37.2 bits (86), Expect = 0.004
 Identities = 17/61 (27%), Positives = 29/61 (47%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           +FV  L  +  +E +  HF++FG++       DKS  + K   F+ F+ +      LKN 
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63

Query: 247 K 247
            
Sbjct: 64  P 64

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|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 9/50 (18%)

Query: 603 VDKIT-EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            DK++ E+L+E FSKYG+I  ++L         +G+ F+ F + E    A
Sbjct: 10  TDKVSKEDLEEIFSKYGKILGISLH--------KGYGFVQFDNEEDARAA 51

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|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 7/59 (11%)

Query: 100 NKMVSHPGIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
              V   G+   +TE+ L  HFS+YG + +V +       R RG A + F   E+ + A
Sbjct: 7   TNCVWLDGLDESVTEQYLTRHFSRYGPVVHVVID------RQRGQALVFFDKVEAAQAA 59

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 9/51 (17%)

Query: 602 IVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +    TEE L+E FS+YGE+E V    D        +AF+ F++ +   KA
Sbjct: 9   LPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKA 51

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|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 = 36.1 bits (84), Expect = 0.004
 Identities = 17/37 (45%), Positives = 25/37 (67%), Gaps = 5/37 (13%)

Query: 114 EELKEHFSKYGEIENVTL--KSDPNTGRSRGFAFIVF 148
           +EL+E FS +G++++V L  K D   G  RGFAF+ F
Sbjct: 15  KELRELFSPFGQVKSVRLPKKFD---GSHRGFAFVEF 48

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|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 = 36.1 bits (84), Expect = 0.004
 Identities = 17/37 (45%), Positives = 25/37 (67%), Gaps = 5/37 (13%)

Query: 608 EELKEHFSKYGEIENVTL--KSDPNTGRSRGFAFIVF 642
           +EL+E FS +G++++V L  K D   G  RGFAF+ F
Sbjct: 15  KELRELFSPFGQVKSVRLPKKFD---GSHRGFAFVEF 48

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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 36.2 bits (83), Expect = 0.004
 Identities = 18/44 (40%), Positives = 25/44 (56%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           EE +  F   GEIE+  L  D  TG+S G+ F+ + D +  EKA
Sbjct: 17  EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 36.2 bits (83), Expect = 0.004
 Identities = 18/44 (40%), Positives = 25/44 (56%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           EE +  F   GEIE+  L  D  TG+S G+ F+ + D +  EKA
Sbjct: 17  EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	661
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	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
KOG0145|consensus	360		100.0
KOG0123|consensus	369		100.0
KOG0127|consensus	678		100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
KOG0148|consensus	321		100.0
KOG0117|consensus	506		100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
KOG0144|consensus	510		100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.98
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.97
KOG0127|consensus	678		99.97
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.97
KOG0117|consensus	506		99.96
KOG0123|consensus	369		99.96
KOG0148|consensus	321		99.96
KOG0110|consensus	725		99.96
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
KOG0145|consensus	360		99.95
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.94
KOG4211|consensus	510		99.94
KOG0144|consensus	510		99.93
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.93
KOG4212|consensus	608		99.91
KOG0131|consensus	203		99.9
KOG0124|consensus	544		99.89
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.89
KOG0110|consensus	725		99.88
KOG4205|consensus	311		99.86
KOG4211|consensus	510		99.85
KOG0147|consensus	549		99.83
KOG0109|consensus	346		99.82
KOG0146|consensus	371		99.82
KOG1190|consensus	492		99.82
KOG4205|consensus	311		99.81
KOG1456|consensus	494		99.8
KOG4212|consensus	608		99.78
KOG0146|consensus	371		99.78
KOG0147|consensus	549		99.77
KOG0124|consensus	544		99.75
KOG0131|consensus	203		99.74
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.73
KOG0109|consensus	346		99.7
KOG1190|consensus	492		99.65
KOG0105|consensus	241		99.62
KOG0105|consensus	241		99.58
KOG1365|consensus	508		99.5
KOG0149|consensus	247		99.5
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.49
KOG4206|consensus	221		99.45
KOG4307|consensus	944		99.42
KOG0149|consensus	247		99.41
KOG1548|consensus	382		99.38
KOG0122|consensus	270		99.38
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.38
KOG0120|consensus	500		99.37
KOG0121|consensus	153		99.36
KOG0120|consensus	500		99.33
KOG0122|consensus	270		99.33
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.31
KOG0107|consensus	195		99.31
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.29
KOG0106|consensus	216		99.29
KOG4207|consensus	256		99.27
PLN03120	260	nucleic acid binding protein; Provisional	99.27
KOG4206|consensus	221		99.26
KOG0125|consensus	376		99.24
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.21
KOG0114|consensus	124		99.2
KOG0113|consensus	335		99.2
KOG0121|consensus	153		99.2
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.18
KOG0125|consensus	376		99.16
KOG0113|consensus	335		99.16
KOG0126|consensus	219		99.14
KOG0126|consensus	219		99.14
PLN03121	243	nucleic acid binding protein; Provisional	99.13
KOG0130|consensus	170		99.13
KOG1457|consensus	284		99.13
KOG0114|consensus	124		99.12
KOG4207|consensus	256		99.12
KOG4307|consensus	944		99.12
KOG1457|consensus	284		99.11
KOG1456|consensus	494		99.11
smart00362	72	RRM_2 RNA recognition motif.	99.09
PLN03120	260	nucleic acid binding protein; Provisional	99.09
PLN03213	759	repressor of silencing 3; Provisional	99.09
smart00360	71	RRM RNA recognition motif.	99.08
KOG0128|consensus	881		99.07
KOG1365|consensus	508		99.06
smart00360	71	RRM RNA recognition motif.	99.04
KOG0130|consensus	170		99.04
KOG0107|consensus	195		99.03
KOG0116|consensus	419		99.02
KOG0111|consensus	298		99.01
KOG0129|consensus	520		99.0
smart00361	70	RRM_1 RNA recognition motif.	99.0
KOG0106|consensus	216		99.0
PLN03121	243	nucleic acid binding protein; Provisional	98.99
smart00362	72	RRM_2 RNA recognition motif.	98.99
PLN03213	759	repressor of silencing 3; Provisional	98.96
KOG0111|consensus	298		98.95
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.94
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.93
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.9
KOG0108|consensus	435		98.9
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.89
KOG0415|consensus	479		98.84
KOG0108|consensus	435		98.83
smart00361	70	RRM_1 RNA recognition motif.	98.83
KOG0128|consensus	881		98.8
KOG4210|consensus	285		98.79
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.78
KOG4208|consensus	214		98.69
KOG0415|consensus	479		98.68
KOG4208|consensus	214		98.67
KOG4660|consensus	549		98.66
KOG4454|consensus	267		98.66
KOG0153|consensus	377		98.57
KOG1548|consensus	382		98.54
KOG0226|consensus	290		98.53
KOG0132|consensus	894		98.51
KOG0112|consensus	975		98.44
KOG0226|consensus	290		98.38
KOG0132|consensus	894		98.25
KOG0153|consensus	377		98.23
KOG4661|consensus	940		98.22
KOG0533|consensus	243		98.19
KOG4660|consensus	549		98.16
KOG0116|consensus	419		98.16
KOG4210|consensus	285		98.09
KOG0533|consensus	243		98.08
KOG4454|consensus	267		98.05
KOG4209|consensus	231		98.03
KOG0129|consensus	520		98.01
KOG4661|consensus	940		98.01
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.95
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.92
KOG4676|consensus	479		97.91
KOG0151|consensus	877		97.68
KOG1995|consensus	351		97.67
KOG4209|consensus	231		97.64
KOG0151|consensus	877		97.61
KOG4849|consensus	498		97.6
KOG4676|consensus	479		97.54
KOG2193|consensus	584		97.53
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.37
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.36
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.33
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.24
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.95
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.86
KOG1995|consensus	351		96.79
KOG0115|consensus	275		96.78
KOG0112|consensus	975		96.77
KOG2314|consensus	698		96.73
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	96.5
KOG2193|consensus	584		96.48
KOG2314|consensus	698		96.46
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.1
KOG0115|consensus	275		96.09
KOG1855|consensus	484		96.08
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.06
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	95.32
KOG1855|consensus	484		95.25
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.19
KOG4849|consensus	498		95.05
KOG3152|consensus	278		95.02
KOG2202|consensus	260		94.87
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.81
KOG3973|consensus	465		94.64
KOG3152|consensus	278		94.28
KOG2591|consensus	684		94.24
KOG2135|consensus	526		94.22
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	93.75
KOG2202|consensus	260		93.68
KOG1996|consensus	378		93.3
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	93.14
KOG1996|consensus	378		93.13
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	93.08
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.08
KOG0921|consensus	1282		91.72
KOG0921|consensus	1282		90.71
KOG2135|consensus	526		89.98
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	89.41
KOG4285|consensus	350		88.79
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	88.33
KOG2068|consensus	327		88.07
KOG2591|consensus	684		87.19
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	85.78
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	84.76
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	84.07
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	82.7
KOG2416|consensus	718		81.46
KOG2068|consensus	327		80.73
KOG2416|consensus	718		80.32

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

Probab=100.00  E-value=1e-45  Score=417.52  Aligned_cols=333  Identities=23%  Similarity=0.335  Sum_probs=270.0

Q ss_pred             EEEcCC-CcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhh
Q psy15852        103 VSHPGI-VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAK  181 (661)
Q Consensus       103 ~~~~~~-~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~  181 (661)
                      |||+++ +++||++|+++|++||+|.+|+|++|+.|++++|||||+|.+.++|++|    +..+++..|.|++|.|.|+.
T Consensus         3 l~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~A----l~~ln~~~i~gk~i~i~~s~   78 (562)
T TIGR01628         3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERA----LETMNFKRLGGKPIRIMWSQ   78 (562)
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHH----HHHhCCCEECCeeEEeeccc
Confidence            455555 5999999999999999999999999999999999999999999999999    88999999999999998875


Q ss_pred             cc-------CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCe
Q psy15852        182 AK-------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDK  253 (661)
Q Consensus       182 ~~-------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~  253 (661)
                      ..       ..+|||+|||.++++++|+++|++||.|.+|+++.+. +++++|||||+|.+.++|.+|++.+ +..+.++
T Consensus        79 ~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~  157 (562)
T TIGR01628        79 RDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDK  157 (562)
T ss_pred             ccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHhcccEecCc
Confidence            32       3579999999999999999999999999999999875 5889999999999999999999887 6789999


Q ss_pred             EEEEEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCC
Q psy15852        254 EVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQA  333 (661)
Q Consensus       254 ~i~V~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  333 (661)
                      .|.|.....+.++..                                                                 
T Consensus       158 ~i~v~~~~~~~~~~~-----------------------------------------------------------------  172 (562)
T TIGR01628       158 EVYVGRFIKKHEREA-----------------------------------------------------------------  172 (562)
T ss_pred             eEEEecccccccccc-----------------------------------------------------------------
Confidence            999977655432100                                                                 


Q ss_pred             CCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccC
Q psy15852        334 TPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKT  413 (661)
Q Consensus       334 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~  413 (661)
                       ..                                                .....++++.++.+++++++|+++|..| 
T Consensus       173 -~~------------------------------------------------~~~~~~l~V~nl~~~~tee~L~~~F~~f-  202 (562)
T TIGR01628       173 -AP------------------------------------------------LKKFTNLYVKNLDPSVNEDKLRELFAKF-  202 (562)
T ss_pred             -cc------------------------------------------------ccCCCeEEEeCCCCcCCHHHHHHHHHhc-
Confidence             00                                                0001234555555669999999999888 


Q ss_pred             cccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHh-CCCCcCC----CcE
Q psy15852        414 TTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK-NPKQKIN----DKE  488 (661)
Q Consensus       414 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~-~~~~~l~----g~~  488 (661)
                                                   |+|.++.+..+. +++++|||||.|.+.++|.+|++ .++..+.    |+.
T Consensus       203 -----------------------------G~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~  252 (562)
T TIGR01628       203 -----------------------------GEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKK  252 (562)
T ss_pred             -----------------------------CCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCcEeccccccee
Confidence                                         789999998874 67889999999999999999994 5567777    888


Q ss_pred             EEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCccccccccccCCCCCc
Q psy15852        489 VDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLT  568 (661)
Q Consensus       489 i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~  568 (661)
                      |.|.++..+.++...                                                       ..    ..  
T Consensus       253 l~v~~a~~k~er~~~-------------------------------------------------------~~----~~--  271 (562)
T TIGR01628       253 LYVGRAQKRAEREAE-------------------------------------------------------LR----RK--  271 (562)
T ss_pred             eEeecccChhhhHHH-------------------------------------------------------HH----hh--
Confidence            888777655332100                                                       00    00  


Q ss_pred             ccCCCccccccCCCCccccccccCCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHH
Q psy15852        569 VSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESL  648 (661)
Q Consensus       569 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A  648 (661)
                              . .  ............++|||+|||+++|+++|+++|++||.|.+|+|++| .+|+++|||||+|.+.++|
T Consensus       272 --------~-~--~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A  339 (562)
T TIGR01628       272 --------F-E--ELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEA  339 (562)
T ss_pred             --------H-H--hhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHH
Confidence                    0 0  00000000123568999999999999999999999999999999999 5699999999999999999


Q ss_pred             HHHHHhCCcc
Q psy15852        649 EKASVEDVYF  658 (661)
Q Consensus       649 ~~A~~~~~~~  658 (661)
                      .+|+.++|..
T Consensus       340 ~~A~~~~~g~  349 (562)
T TIGR01628       340 NRAVTEMHGR  349 (562)
T ss_pred             HHHHHHhcCC
Confidence            9999987754

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=4e-39  Score=354.95  Aligned_cols=413  Identities=15%  Similarity=0.134  Sum_probs=254.8

Q ss_pred             cEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHH--hCCeeecceeehh
Q psy15852        101 KMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIA--EGNHVINNKKIEA  177 (661)
Q Consensus       101 ~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~--~~~~~i~g~~i~v  177 (661)
                      ++|+|+|+| ++++++|+++|++||+|.+|+|+++      ||||||+|.+.++|++|    +..  +++..|.|++|.|
T Consensus         3 ~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~A----i~~~~~~~~~l~g~~l~v   72 (481)
T TIGR01649         3 PVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKAC----VNFATSVPIYIRGQPAFF   72 (481)
T ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHH----HHHhhcCCceEcCeEEEE
Confidence            455666655 9999999999999999999999863      57999999999999998    654  5789999999999


Q ss_pred             hhhhccC-----------------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHH
Q psy15852        178 KKAKAKS-----------------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVI  240 (661)
Q Consensus       178 ~~~~~~~-----------------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~  240 (661)
                      .++..+.                 .+|||.||++.+++++|+++|++||.|.+|.++++..    +++|||+|.+.++|.
T Consensus        73 ~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~  148 (481)
T TIGR01649        73 NYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQ  148 (481)
T ss_pred             EecCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC----ceEEEEEECCHHHHH
Confidence            8764211                 2699999999999999999999999999999987542    478999999999999


Q ss_pred             HHHHhC-CCccCC--eEEEEEeccCCCCCCC--CCCCCCCCC----------CCCCCCCCCCCCCC--CCCCCCCCCCCC
Q psy15852        241 DLLKNP-KQKIND--KEVDVKKATPKPEPFG--VRGGRGGRG----------GRGGRGGRMAGGYG--GYGGYGGGYGGI  303 (661)
Q Consensus       241 ~Al~~~-~~~~~g--~~i~V~~a~~k~~~~~--~~~~~~~~g----------~~~g~~~~~~~~~g--~~~g~~~~~~~~  303 (661)
                      +|++.+ +..|.+  +.|+|.|++...-.-.  ....+..-+          .............+  ...+...||+..
T Consensus       149 ~A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  228 (481)
T TIGR01649       149 HAKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSH  228 (481)
T ss_pred             HHHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccC
Confidence            999987 566654  5899998876432100  000000000          00000000000000  000111111111


Q ss_pred             --CCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccc
Q psy15852        304 --LYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSY  381 (661)
Q Consensus       304 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  381 (661)
                        .+.+  .+....++.... ...+..+.+.. .+.+.     .+       .                         .+
T Consensus       229 ~~~~~~--~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~-----~~-------~-------------------------~~  267 (481)
T TIGR01649       229 GGPLAP--LAGGDRMGPPHG-PPSRYRPAYEA-APLAP-----AI-------S-------------------------SY  267 (481)
T ss_pred             CCCCCc--ccccccCCCccc-CCCCCcccccc-cccCc-----cc-------c-------------------------cc
Confidence              0000  000000000000 00000000000 00000     00       0                         00


Q ss_pred             ccc-ccccccccccCCCCC-cCccchhhhhhccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcc
Q psy15852        382 REW-GHVADNLLLCDNFPS-IRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQR  459 (661)
Q Consensus       382 ~~~-g~~~~~~~~~~~~p~-~~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~  459 (661)
                      ... ..-..++++.++.+. +++++|+++|..|                              |+|..|+++.+     .
T Consensus       268 ~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~y------------------------------G~V~~vki~~~-----~  312 (481)
T TIGR01649       268 GPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVY------------------------------GNVERVKFMKN-----K  312 (481)
T ss_pred             CCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhc------------------------------CCeEEEEEEeC-----C
Confidence            000 011234555555553 9999999999998                              78999999875     3


Q ss_pred             cceEEEEeCChHHHHHHHh-CCCCcCCCcEEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy15852        460 KNFCFITFEHESVVIDLLK-NPKQKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELD  538 (661)
Q Consensus       460 ~g~aFV~F~~~e~A~~Ai~-~~~~~l~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~~~~~~  538 (661)
                      +|||||+|.+.++|+.|+. +++..|.|+.|.|..+..........+.. .            .+..+       +    
T Consensus       313 ~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~-~------------~~~~~-------~----  368 (481)
T TIGR01649       313 KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQL-D------------DGLTS-------Y----  368 (481)
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcC-c------------CCCcc-------c----
Confidence            6999999999999999994 67788999999998876542211100000 0            00000       0    


Q ss_pred             CccccccccccCCCccccccccccCCCCCcccCCCccccccCCCCccccccccCCCeEEEcCCCCCCCHHHHHHHhhcCC
Q psy15852        539 YLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYG  618 (661)
Q Consensus       539 ~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~te~dL~~~F~~~G  618 (661)
                             .+...+...       ....|.               ............+|||+|||+++||++|+++|+.||
T Consensus       369 -------~d~~~~~~~-------r~~~~~---------------~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G  419 (481)
T TIGR01649       369 -------KDYSSSRNH-------RFKKPG---------------SANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENG  419 (481)
T ss_pred             -------ccccCCccc-------cCCCcc---------------cccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcC
Confidence                   000000000       000000               000001123457899999999999999999999999


Q ss_pred             C--eeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        619 E--IENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       619 ~--I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      .  |.+|++..+.. + ++|+|||+|.+.++|.+|+..+|+.
T Consensus       420 ~~~i~~ik~~~~~~-~-~~~~gfVeF~~~e~A~~Al~~ln~~  459 (481)
T TIGR01649       420 VHKVKKFKFFPKDN-E-RSKMGLLEWESVEDAVEALIALNHH  459 (481)
T ss_pred             CccceEEEEecCCC-C-cceeEEEEcCCHHHHHHHHHHhcCC
Confidence            8  88898876542 3 5899999999999999999987764

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).

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

Probab=100.00  E-value=9.5e-39  Score=360.86  Aligned_cols=325  Identities=18%  Similarity=0.268  Sum_probs=253.8

Q ss_pred             eEEeCCCCCCCCcHHHHHHHh-hhccccccccEEeecCCCCc------eeeecccc----------cccccccccceeee
Q psy15852         32 KLFCPLSSYLELDYLQLWQYF-DWVSSSFSENCLLEDSIGKP------LTVSCSHH----------YYLFDQILRTHFFY   94 (661)
Q Consensus        32 ~lfVg~l~~~~te~~~l~~~F-~~g~~~~~~~~~~~d~~~~~------~~~~~~~~----------~~l~~~~~r~~~~~   94 (661)
                      .|||||||+++|| ++|+++| ++|  .|.+|.+++|..+..      |.|...+.          ..+.++.++..|..
T Consensus         2 sl~VgnLp~~vte-~~L~~~F~~~G--~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~   78 (562)
T TIGR01628         2 SLYVGDLDPDVTE-AKLYDLFKPFG--PVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQ   78 (562)
T ss_pred             eEEEeCCCCCCCH-HHHHHHHHhcC--CEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccc
Confidence            6999999999999 9999999 999  999999999987543      34333322          12333444555542


Q ss_pred             eec----CCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCee
Q psy15852         95 IME----AKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV  169 (661)
Q Consensus        95 ~~~----~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~  169 (661)
                      ...    .....|+++|++ ++++++|+++|++||.|.+|+|+.+. +|+++|||||+|.+.++|++|    +..+++..
T Consensus        79 ~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~A----i~~lng~~  153 (562)
T TIGR01628        79 RDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAA----IQKVNGML  153 (562)
T ss_pred             ccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHH----HHHhcccE
Confidence            111    112345555555 99999999999999999999999986 589999999999999999999    89999999


Q ss_pred             ecceeehhhhhhcc----------CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHH
Q psy15852        170 INNKKIEAKKAKAK----------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVV  239 (661)
Q Consensus       170 i~g~~i~v~~~~~~----------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A  239 (661)
                      +.++.|.|.....+          .++|||+|||.++++++|+++|++||.|.++.++.+. +++++|||||+|.+.++|
T Consensus       154 ~~~~~i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~-~g~~~G~afV~F~~~e~A  232 (562)
T TIGR01628       154 LNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDA  232 (562)
T ss_pred             ecCceEEEeccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHH
Confidence            99999988654332          2569999999999999999999999999999999885 588999999999999999


Q ss_pred             HHHHHhC-CCccC----CeEEEEEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccc
Q psy15852        240 IDLLKNP-KQKIN----DKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELN  314 (661)
Q Consensus       240 ~~Al~~~-~~~~~----g~~i~V~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~  314 (661)
                      .+|++.+ +..+.    |+.|.|.++..+.++..                                              
T Consensus       233 ~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~----------------------------------------------  266 (562)
T TIGR01628       233 AKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREA----------------------------------------------  266 (562)
T ss_pred             HHHHHHhCCcEecccccceeeEeecccChhhhHH----------------------------------------------
Confidence            9999987 57788    99999988876543200                                              


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccc-cccccccc
Q psy15852        315 ELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWG-HVADNLLL  393 (661)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g-~~~~~~~~  393 (661)
                                                                              .++..+......... ....++++
T Consensus       267 --------------------------------------------------------~~~~~~~~~~~~~~~~~~~~~l~V  290 (562)
T TIGR01628       267 --------------------------------------------------------ELRRKFEELQQERKMKAQGVNLYV  290 (562)
T ss_pred             --------------------------------------------------------HHHhhHHhhhhhhhcccCCCEEEE
Confidence                                                                    000000000000000 01123555


Q ss_pred             cCCCCCcCccchhhhhhccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHH
Q psy15852        394 CDNFPSIRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVV  473 (661)
Q Consensus       394 ~~~~p~~~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A  473 (661)
                      .++.+.+++++|+++|+.|                              |+|.+|++..| .+++++|||||+|.+.++|
T Consensus       291 ~nl~~~~~~~~L~~~F~~~------------------------------G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A  339 (562)
T TIGR01628       291 KNLDDTVTDEKLRELFSEC------------------------------GEITSAKVMLD-EKGVSRGFGFVCFSNPEEA  339 (562)
T ss_pred             eCCCCccCHHHHHHHHHhc------------------------------CCeEEEEEEEC-CCCCcCCeEEEEeCCHHHH
Confidence            5555569999999999988                              78999999998 7789999999999999999


Q ss_pred             HHHH-hCCCCcCCCcEEEEecCCCCC
Q psy15852        474 IDLL-KNPKQKINDKEVDVKKATPKP  498 (661)
Q Consensus       474 ~~Ai-~~~~~~l~g~~i~v~~a~~~~  498 (661)
                      .+|+ ..++..++|+.|.|.+|..+.
T Consensus       340 ~~A~~~~~g~~~~gk~l~V~~a~~k~  365 (562)
T TIGR01628       340 NRAVTEMHGRMLGGKPLYVALAQRKE  365 (562)
T ss_pred             HHHHHHhcCCeeCCceeEEEeccCcH
Confidence            9999 466688999999999998764

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=1e-37  Score=333.05  Aligned_cols=317  Identities=16%  Similarity=0.175  Sum_probs=209.4

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      ..+|||+|||..+++++|+++|++||+|.+|+|++++.+|+++|||||+|.+.++|.+||+.+ +..+.|+.|.|.++.+
T Consensus         3 ~~~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~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            468999999999999999999999999999999999999999999999999999999999987 6789999999999875


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCC
Q psy15852        263 KPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDV  342 (661)
Q Consensus       263 k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  342 (661)
                      +....                                                                           
T Consensus        83 ~~~~~---------------------------------------------------------------------------   87 (352)
T TIGR01661        83 SSDSI---------------------------------------------------------------------------   87 (352)
T ss_pred             ccccc---------------------------------------------------------------------------
Confidence            43210                                                                           


Q ss_pred             CccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCCcc
Q psy15852        343 TGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTE  422 (661)
Q Consensus       343 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~  422 (661)
                                                                  ....+++.++.+.+++++|+.+|..+          
T Consensus        88 --------------------------------------------~~~~l~v~~l~~~~~~~~l~~~f~~~----------  113 (352)
T TIGR01661        88 --------------------------------------------KGANLYVSGLPKTMTQHELESIFSPF----------  113 (352)
T ss_pred             --------------------------------------------ccceEEECCccccCCHHHHHHHHhcc----------
Confidence                                                        01134555555568999999999888          


Q ss_pred             cchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHH-hCCCCcCCC--cEEEEecCCCCCC
Q psy15852        423 HMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL-KNPKQKIND--KEVDVKKATPKPE  499 (661)
Q Consensus       423 ~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai-~~~~~~l~g--~~i~v~~a~~~~~  499 (661)
                                          |+|..+.++.+..++.++|||||+|.+.++|+.|+ .+++..+.|  ..|.|.++.....
T Consensus       114 --------------------G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~~  173 (352)
T TIGR01661       114 --------------------GQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSS  173 (352)
T ss_pred             --------------------CCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCCc
Confidence                                78999999999989999999999999999999999 455566665  5688888765432


Q ss_pred             CCCCCCC------CCCCCCCCCCCCC-CCCCCC----CCCCCCCCCCC-CCCccccccccccCCCccccccccccCCCCC
Q psy15852        500 PFGVRGG------RGGRGGRGGRGGR-MAGGYG----GYGGYGGGYGE-LDYLQLWQFFDWISSSFSENCLLEDSIGKPL  567 (661)
Q Consensus       500 ~~~~~~~------~~~~~~~~~~~~~-~~~g~g----g~~~~g~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~  567 (661)
                      .......      ............. ...+.+    ....+....+. ..+..... ......     .........|.
T Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~-----~~~~~~~~~~~  247 (352)
T TIGR01661       174 SNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQ-QQHAVA-----QQHAAQRASPP  247 (352)
T ss_pred             CCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhh-hhcccc-----cccccccCCCc
Confidence            2110000      0000000000000 000000    00000000000 00000000 000000     00000000000


Q ss_pred             cccCCCccccccCCCCccccccccCCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHH
Q psy15852        568 TVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES  647 (661)
Q Consensus       568 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~  647 (661)
                      ........  ..  ...........+.+|||+|||+++++++|+++|++||.|++|+|++|+.||++||||||+|.+.++
T Consensus       248 ~~~~~~~~--~~--~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~  323 (352)
T TIGR01661       248 ATDGQTAG--LA--AGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDE  323 (352)
T ss_pred             cccccccc--cc--cCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHH
Confidence            00000000  00  000000111234579999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhCCccc
Q psy15852        648 LEKASVEDVYFY  659 (661)
Q Consensus       648 A~~A~~~~~~~~  659 (661)
                      |.+||+.++.+.
T Consensus       324 A~~Ai~~lnG~~  335 (352)
T TIGR01661       324 AAMAILSLNGYT  335 (352)
T ss_pred             HHHHHHHhCCCE
Confidence            999999988754

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=3.5e-37  Score=328.84  Aligned_cols=335  Identities=18%  Similarity=0.179  Sum_probs=221.9

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .+|+|.+|+++++|++|+++|++||+|.+|+|++++.+|+++|||||+|.++++|++|    +..+++..|.|+.|.|.+
T Consensus         4 ~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~A----i~~l~g~~l~g~~i~v~~   79 (352)
T TIGR01661         4 TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA----VNSLNGLRLQNKTIKVSY   79 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHH----HhhcccEEECCeeEEEEe
Confidence            4455555555999999999999999999999999999999999999999999999999    889999999999999988


Q ss_pred             hhcc-----CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC-
Q psy15852        180 AKAK-----SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND-  252 (661)
Q Consensus       180 ~~~~-----~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g-  252 (661)
                      +.+.     .++|||+|||..+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|++|++.+ +..+.| 
T Consensus        80 a~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~  159 (352)
T TIGR01661        80 ARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGC  159 (352)
T ss_pred             ecccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCC
Confidence            7654     368999999999999999999999999999999998888899999999999999999999987 456655 


Q ss_pred             -eEEEEEeccCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCC--CCCCCCccccccccCCCCCCCCCCCCC
Q psy15852        253 -KEVDVKKATPKPEPFGVRGGRGGRGGRGGRG-GRMAGGYGGYGGYGGGYG--GILYKPLLFYELNELGISGRSLVCRTG  328 (661)
Q Consensus       253 -~~i~V~~a~~k~~~~~~~~~~~~~g~~~g~~-~~~~~~~g~~~g~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~  328 (661)
                       ++|.|.++..+....... -........... ..........++..+...  ...+.+.....   +............
T Consensus       160 ~~~i~v~~a~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~  235 (352)
T TIGR01661       160 TEPITVKFANNPSSSNSKG-LLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDF---TAVLAHQQQQHAV  235 (352)
T ss_pred             ceeEEEEECCCCCcCCchh-cCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchh---hhhhhhhhhhccc
Confidence             678999887654321100 000000000000 000000000000000000  00000000000   0000000000000


Q ss_pred             CCCCCCCCCcccCCCc-cEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhh
Q psy15852        329 PMVQATPPLAEVDVTG-VIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPE  407 (661)
Q Consensus       329 ~~~~~~~~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~  407 (661)
                      +......+........ ......+....                           ....-..+++|.++.+.+++++|++
T Consensus       236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~lfV~NL~~~~~e~~L~~  288 (352)
T TIGR01661       236 AQQHAAQRASPPATDGQTAGLAAGAQIA---------------------------ASDGAGYCIFVYNLSPDTDETVLWQ  288 (352)
T ss_pred             ccccccccCCCccccccccccccCCCCC---------------------------CCCCCCcEEEEeCCCCCCCHHHHHH
Confidence            0000000000000000 00000000000                           0000112466666666699999999


Q ss_pred             hhhccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHh-CCCCcCCC
Q psy15852        408 AFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK-NPKQKIND  486 (661)
Q Consensus       408 ~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~-~~~~~l~g  486 (661)
                      +|++|                              |.|.+++++.|..+++++|||||+|.+.++|..||. +++..|+|
T Consensus       289 ~F~~f------------------------------G~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~g  338 (352)
T TIGR01661       289 LFGPF------------------------------GAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGN  338 (352)
T ss_pred             HHHhC------------------------------CCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECC
Confidence            99998                              779999999999999999999999999999999994 67789999


Q ss_pred             cEEEEecCCCCCC
Q psy15852        487 KEVDVKKATPKPE  499 (661)
Q Consensus       487 ~~i~v~~a~~~~~  499 (661)
                      +.|.|.+++.+..
T Consensus       339 r~i~V~~~~~~~~  351 (352)
T TIGR01661       339 RVLQVSFKTNKAY  351 (352)
T ss_pred             eEEEEEEccCCCC
Confidence            9999999988753

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>KOG0145|consensus

Probab=100.00  E-value=3.3e-38  Score=295.55  Aligned_cols=163  Identities=26%  Similarity=0.411  Sum_probs=149.6

Q ss_pred             cCCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceee
Q psy15852         97 EAKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKI  175 (661)
Q Consensus        97 ~~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i  175 (661)
                      +..++.++++-+| .+|++||+.+|...|+|++|++++||.+|+|.||+||.|.+++||++|    +..+||..+..+.|
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~A----intlNGLrLQ~KTI  113 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKA----INTLNGLRLQNKTI  113 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHH----HhhhcceeeccceE
Confidence            4456777777777 999999999999999999999999999999999999999999999999    99999999999999


Q ss_pred             hhhhhhccC-----CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC-Cc
Q psy15852        176 EAKKAKAKS-----GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK-QK  249 (661)
Q Consensus       176 ~v~~~~~~~-----~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~-~~  249 (661)
                      +|.+++|.+     .+|||++||..+|..+|+++|++||.|..-+|+.|..||.++|.+||.|+..++|+.||+.++ ++
T Consensus       114 KVSyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~  193 (360)
T KOG0145|consen  114 KVSYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQK  193 (360)
T ss_pred             EEEeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCC
Confidence            999998764     789999999999999999999999999999999999999999999999999999999999974 44


Q ss_pred             cCC--eEEEEEeccCC
Q psy15852        250 IND--KEVDVKKATPK  263 (661)
Q Consensus       250 ~~g--~~i~V~~a~~k  263 (661)
                      --|  .+|.|+++...
T Consensus       194 P~g~tepItVKFannP  209 (360)
T KOG0145|consen  194 PSGCTEPITVKFANNP  209 (360)
T ss_pred             CCCCCCCeEEEecCCc
Confidence            433  68999998754

>KOG0123|consensus

Probab=100.00  E-value=3.6e-36  Score=314.81  Aligned_cols=329  Identities=22%  Similarity=0.286  Sum_probs=262.6

Q ss_pred             EEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhh
Q psy15852        102 MVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAK  181 (661)
Q Consensus       102 ~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~  181 (661)
                      .+|++  |++||..|.++|+.+|+|.+|+|++|. |  +-|||||.|.++++|++|    +.++|...+.|++|++.|+.
T Consensus         3 sl~vg--~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A----~~~~n~~~~~~~~~rim~s~   73 (369)
T KOG0123|consen    3 SLYVG--PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERA----LDTMNFDVLKGKPIRIMWSQ   73 (369)
T ss_pred             ceecC--CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHH----HHHcCCcccCCcEEEeehhc
Confidence            46777  999999999999999999999999998 6  999999999999999999    99999999999999999999


Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      .....|||+||+++++..+|.++|+.||+|.+|++..+.. | ++|| ||+|+++++|.+|+..+ +..+.+++|.|...
T Consensus        74 rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~  150 (369)
T KOG0123|consen   74 RDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLF  150 (369)
T ss_pred             cCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeec
Confidence            9888899999999999999999999999999999999876 4 8999 99999999999999997 67899999999999


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCccc
Q psy15852        261 TPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEV  340 (661)
Q Consensus       261 ~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (661)
                      ..+.++..+-                                                                   .+ 
T Consensus       151 ~~~~er~~~~-------------------------------------------------------------------~~-  162 (369)
T KOG0123|consen  151 ERKEEREAPL-------------------------------------------------------------------GE-  162 (369)
T ss_pred             cchhhhcccc-------------------------------------------------------------------cc-
Confidence            8877642110                                                                   00 


Q ss_pred             CCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCC
Q psy15852        341 DVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTT  420 (661)
Q Consensus       341 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~  420 (661)
                      .                               +..+            .+.++.+..-.+++++|..+|..+        
T Consensus       163 ~-------------------------------~~~~------------t~v~vk~~~~~~~~~~l~~~f~~~--------  191 (369)
T KOG0123|consen  163 Y-------------------------------KKRF------------TNVYVKNLEEDSTDEELKDLFSAY--------  191 (369)
T ss_pred             h-------------------------------hhhh------------hhhheeccccccchHHHHHhhccc--------
Confidence            0                               0000            011112122236777777777776        


Q ss_pred             cccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHhCCC-CcCCCcEEEEecCCCCCC
Q psy15852        421 TEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK-QKINDKEVDVKKATPKPE  499 (661)
Q Consensus       421 ~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~~~~-~~l~g~~i~v~~a~~~~~  499 (661)
                                            |.|.++.++.+.... +++|+||.|.++++|..|+..+. ..+.+..+.|..+..+.+
T Consensus       192 ----------------------g~i~s~~v~~~~~g~-~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e  248 (369)
T KOG0123|consen  192 ----------------------GSITSVAVMRDSIGK-SKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKKSE  248 (369)
T ss_pred             ----------------------CcceEEEEeecCCCC-CCCccceeecChhHHHHHHHhccCCcCCccceeecccccchh
Confidence                                  779999998876654 89999999999999999995554 556678888876665322


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCccccccccccCCCCCcccCCCcccccc
Q psy15852        500 PFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFD  579 (661)
Q Consensus       500 ~~~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~  579 (661)
                      ...                                                                    +........
T Consensus       249 ~~~--------------------------------------------------------------------~l~~~~~~~  260 (369)
T KOG0123|consen  249 REA--------------------------------------------------------------------ELKRKFEQE  260 (369)
T ss_pred             hHH--------------------------------------------------------------------HHhhhhHhh
Confidence            110                                                                    000000000


Q ss_pred             CCCCccccccccCCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        580 QNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       580 ~~~~~~~~~~~~~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      .    ...........|||.|+...++++.|+++|+.||+|.+++|+.++. |+++|||||+|.+.++|.+|+...+.
T Consensus       261 ~----~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~~-g~skG~gfV~fs~~eeA~~A~~~~n~  333 (369)
T KOG0123|consen  261 F----AKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDEN-GKSKGFGFVEFSSPEEAKKAMTEMNG  333 (369)
T ss_pred             h----hhccccccccccccccCccccchhHHHHHHhcccceeeEEEEeccC-CCccceEEEEcCCHHHHHHHHHhhCh
Confidence            0    0000012346799999999999999999999999999999999987 99999999999999999999886543

>KOG0127|consensus

Probab=100.00  E-value=3.6e-35  Score=301.10  Aligned_cols=160  Identities=22%  Similarity=0.382  Sum_probs=147.8

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++|+.+++++++.++|.++|+.+|+|..|.++.++.++.+|||+||.|.-.||+++|    +...++..+.|+.|.|..
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA----~~e~~~~kf~Gr~l~v~~   81 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRA----LAETEQSKFEGRILNVDP   81 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHH----HHHhhcCcccceeccccc
Confidence            5788888888999999999999999999999999999899999999999999999999    888999999999999987


Q ss_pred             hhccC-------------------------------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcE
Q psy15852        180 AKAKS-------------------------------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF  228 (661)
Q Consensus       180 ~~~~~-------------------------------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~  228 (661)
                      +..+.                               .+|.|+|||+.+.+.+|+.+|++||.|..|.|++..+++.+ ||
T Consensus        82 A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklc-GF  160 (678)
T KOG0127|consen   82 AKKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLC-GF  160 (678)
T ss_pred             ccccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCcc-ce
Confidence            75432                               57999999999999999999999999999999988875554 99


Q ss_pred             EEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCC
Q psy15852        229 CFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKP  264 (661)
Q Consensus       229 afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~  264 (661)
                      |||+|....+|.+||+.+ ++.|+||+|-|.||.++.
T Consensus       161 aFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  161 AFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             EEEEEeeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence            999999999999999997 589999999999999876

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=100.00  E-value=1.6e-34  Score=315.34  Aligned_cols=246  Identities=20%  Similarity=0.288  Sum_probs=198.4

Q ss_pred             CCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeec-ceeeh
Q psy15852         99 KNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVIN-NKKIE  176 (661)
Q Consensus        99 ~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~-g~~i~  176 (661)
                      ..+.|+|+|+| +++|++|+++|++||+|.+|+|++| .+|++||||||+|.+.++|++|    +..+|+..|. ++.|.
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~A----i~~lng~~i~~Gr~l~  131 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEA----VKLLNNYEIRPGRLLG  131 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHH----HHHcCCCeecCCcccc
Confidence            34556666666 9999999999999999999999999 6799999999999999999999    9999998885 77777


Q ss_pred             hhhhhccCCeeEecCCCccCCHHHHHHHHhcCCC-eEEE-EeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC---CccC
Q psy15852        177 AKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGN-IIET-EMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK---QKIN  251 (661)
Q Consensus       177 v~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~-i~~v-~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~---~~~~  251 (661)
                      |..+. ..++|||+|||.++++++|.+.|++++. +.++ .+.....+++++|||||+|.++++|.+|++.+.   ..+.
T Consensus       132 V~~S~-~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~  210 (578)
T TIGR01648       132 VCISV-DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLW  210 (578)
T ss_pred             ccccc-cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEec
Confidence            77664 3679999999999999999999999863 4444 333444557889999999999999999998762   4689


Q ss_pred             CeEEEEEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCC
Q psy15852        252 DKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMV  331 (661)
Q Consensus       252 g~~i~V~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  331 (661)
                      |+.|.|.|+.++.....                                                               
T Consensus       211 Gr~I~VdwA~p~~~~d~---------------------------------------------------------------  227 (578)
T TIGR01648       211 GHVIAVDWAEPEEEVDE---------------------------------------------------------------  227 (578)
T ss_pred             CceEEEEeecccccccc---------------------------------------------------------------
Confidence            99999999986542100                                                               


Q ss_pred             CCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhc
Q psy15852        332 QATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLT  411 (661)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~  411 (661)
                              ...                                           .-..+|+|.++...+++++|+++|+.
T Consensus       228 --------~~~-------------------------------------------~~~k~LfVgNL~~~~tee~L~~~F~~  256 (578)
T TIGR01648       228 --------DVM-------------------------------------------AKVKILYVRNLMTTTTEEIIEKSFSE  256 (578)
T ss_pred             --------ccc-------------------------------------------ccccEEEEeCCCCCCCHHHHHHHHHh
Confidence                    000                                           00123555555556999999999988


Q ss_pred             cCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHh-CCCCcCCCcEEE
Q psy15852        412 KTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK-NPKQKINDKEVD  490 (661)
Q Consensus       412 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~-~~~~~l~g~~i~  490 (661)
                      |.+                            |+|+.|.++.        +||||+|.+.++|++|++ +++..|.|+.|.
T Consensus       257 f~~----------------------------G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~  300 (578)
T TIGR01648       257 FKP----------------------------GKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIE  300 (578)
T ss_pred             cCC----------------------------CceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence            854                            7799987653        799999999999999995 667899999999


Q ss_pred             EecCCCCCCC
Q psy15852        491 VKKATPKPEP  500 (661)
Q Consensus       491 v~~a~~~~~~  500 (661)
                      |.++.+....
T Consensus       301 V~~Akp~~~~  310 (578)
T TIGR01648       301 VTLAKPVDKK  310 (578)
T ss_pred             EEEccCCCcc
Confidence            9999886543

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.

>KOG0148|consensus

Probab=100.00  E-value=5.4e-34  Score=269.48  Aligned_cols=214  Identities=19%  Similarity=0.320  Sum_probs=184.0

Q ss_pred             CCCceEEeCCCCCCCCcHHHHHHHh-hhccccccccEEeecCCCCceeeecccccccccccccceeeeeecCCCcEEEEc
Q psy15852         28 DDDRKLFCPLSSYLELDYLQLWQYF-DWVSSSFSENCLLEDSIGKPLTVSCSHHYYLFDQILRTHFFYIMEAKNKMVSHP  106 (661)
Q Consensus        28 ~~~r~lfVg~l~~~~te~~~l~~~F-~~g~~~~~~~~~~~d~~~~~~~~~~~~~~~l~~~~~r~~~~~~~~~~~~~~~~~  106 (661)
                      ++.|+||||||+.++|| +-|..+| +.|  .+..|++|.|...  +..++..... ....++.|        .-+|+..
T Consensus         4 ~~prtlyvgnld~~vte-~~i~~lf~qig--~v~~~k~i~~e~~--v~wa~~p~nQ-sk~t~~~h--------fhvfvgd   69 (321)
T KOG0148|consen    4 DEPRTLYVGNLDSTVTE-DFIATLFNQIG--SVTKTKVIFDELK--VNWATAPGNQ-SKPTSNQH--------FHVFVGD   69 (321)
T ss_pred             CCCceEEeeccChhhHH-HHHHHHHHhcc--ccccceeehhhhc--cccccCcccC-CCCccccc--------eeEEehh
Confidence            47899999999999999 9999999 999  9999999998322  2211111100 01111222        3467777


Q ss_pred             CCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhhccC--
Q psy15852        107 GIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKAKS--  184 (661)
Q Consensus       107 ~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~~~~--  184 (661)
                      +.+.++-++|++.|.+||+|.+++|++|.+|++||||+||.|...++|++|    |..+||+-|.+|.|+..|+..+.  
T Consensus        70 ls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnA----I~~MnGqWlG~R~IRTNWATRKp~e  145 (321)
T KOG0148|consen   70 LSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENA----IQQMNGQWLGRRTIRTNWATRKPSE  145 (321)
T ss_pred             cchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHH----HHHhCCeeeccceeeccccccCccc
Confidence            888999999999999999999999999999999999999999999999999    99999999999999999986543  


Q ss_pred             -------------------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHh
Q psy15852        185 -------------------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN  245 (661)
Q Consensus       185 -------------------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~  245 (661)
                                         ++|||+||+.-++|++|++.|++||.|.+|++.++      +|||||+|.+.|+|.+||..
T Consensus       146 ~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~  219 (321)
T KOG0148|consen  146 MNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQ  219 (321)
T ss_pred             cCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHH
Confidence                               89999999999999999999999999999999876      89999999999999999999


Q ss_pred             C-CCccCCeEEEEEeccCCCC
Q psy15852        246 P-KQKINDKEVDVKKATPKPE  265 (661)
Q Consensus       246 ~-~~~~~g~~i~V~~a~~k~~  265 (661)
                      + +.++.|+.+++.|-+....
T Consensus       220 mNntei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  220 MNNTEIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             hcCceeCceEEEEeccccCCC
Confidence            7 6899999999999876543

>KOG0117|consensus

Probab=100.00  E-value=4.4e-33  Score=280.16  Aligned_cols=247  Identities=20%  Similarity=0.316  Sum_probs=204.1

Q ss_pred             CCCcEEEEc-CCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeee-cceee
Q psy15852         98 AKNKMVSHP-GIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVI-NNKKI  175 (661)
Q Consensus        98 ~~~~~~~~~-~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i-~g~~i  175 (661)
                      ...+-|+++ +|.++.|++|..+|++.|+|.+++|++|+.+|.+||||||.|.+.++|++|    |..+|+++| .|+.|
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~A----ik~lnn~Eir~GK~i  156 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEA----IKELNNYEIRPGKLL  156 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHH----HHHhhCccccCCCEe
Confidence            344444444 555999999999999999999999999999999999999999999999999    999999988 57888


Q ss_pred             hhhhhhccCCeeEecCCCccCCHHHHHHHHhcCC-CeEEEEeccCC-CCCCcCcEEEEEeCCHHHHHHHHHhC---CCcc
Q psy15852        176 EAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFG-NIIETEMPYDK-SKSQRKNFCFITFEHESVVIDLLKNP---KQKI  250 (661)
Q Consensus       176 ~v~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G-~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~Al~~~---~~~~  250 (661)
                      .|..+. ..++|||+|||.+.++++|.+.|++.+ -|.+|.+...+ +..++||||||+|.++..|..|-.++   ..++
T Consensus       157 gvc~Sv-an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~kl  235 (506)
T KOG0117|consen  157 GVCVSV-ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKL  235 (506)
T ss_pred             EEEEee-ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceee
Confidence            776554 468999999999999999999999987 46677666544 34789999999999999999998886   4689


Q ss_pred             CCeEEEEEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCC
Q psy15852        251 NDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPM  330 (661)
Q Consensus       251 ~g~~i~V~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  330 (661)
                      +|..+.|.||.++.+..                                                               
T Consensus       236 wgn~~tVdWAep~~e~d---------------------------------------------------------------  252 (506)
T KOG0117|consen  236 WGNAITVDWAEPEEEPD---------------------------------------------------------------  252 (506)
T ss_pred             cCCcceeeccCcccCCC---------------------------------------------------------------
Confidence            99999999999876531                                                               


Q ss_pred             CCCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhh
Q psy15852        331 VQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFL  410 (661)
Q Consensus       331 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~  410 (661)
                              +.....|                                           .+++|.|+.-++|+|.|++.|.
T Consensus       253 --------ed~ms~V-------------------------------------------KvLYVRNL~~~tTeE~lk~~F~  281 (506)
T KOG0117|consen  253 --------EDTMSKV-------------------------------------------KVLYVRNLMESTTEETLKKLFN  281 (506)
T ss_pred             --------hhhhhhe-------------------------------------------eeeeeeccchhhhHHHHHHHHH
Confidence                    0011111                                           2344555555699999999998


Q ss_pred             ccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHH-hCCCCcCCCcEE
Q psy15852        411 TKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL-KNPKQKINDKEV  489 (661)
Q Consensus       411 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai-~~~~~~l~g~~i  489 (661)
                      .|                              |+|+.|+.++        .||||+|.+.++|.+|| ..+...|+|..|
T Consensus       282 ~~------------------------------G~veRVkk~r--------DYaFVHf~eR~davkAm~~~ngkeldG~~i  323 (506)
T KOG0117|consen  282 EF------------------------------GKVERVKKPR--------DYAFVHFAEREDAVKAMKETNGKELDGSPI  323 (506)
T ss_pred             hc------------------------------cceEEeeccc--------ceeEEeecchHHHHHHHHHhcCceecCceE
Confidence            88                              7899999775        59999999999999999 556689999999


Q ss_pred             EEecCCCCCCCC
Q psy15852        490 DVKKATPKPEPF  501 (661)
Q Consensus       490 ~v~~a~~~~~~~  501 (661)
                      +|..|+|.....
T Consensus       324 EvtLAKP~~k~k  335 (506)
T KOG0117|consen  324 EVTLAKPVDKKK  335 (506)
T ss_pred             EEEecCChhhhc
Confidence            999999886543

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=100.00  E-value=3.5e-32  Score=299.84  Aligned_cols=219  Identities=16%  Similarity=0.122  Sum_probs=167.8

Q ss_pred             CceEEeCCCCCCCCcHHHHHHHh-hhccccccccEEeecCCCCceeeecccc------------cccccccccceeeeee
Q psy15852         30 DRKLFCPLSSYLELDYLQLWQYF-DWVSSSFSENCLLEDSIGKPLTVSCSHH------------YYLFDQILRTHFFYIM   96 (661)
Q Consensus        30 ~r~lfVg~l~~~~te~~~l~~~F-~~g~~~~~~~~~~~d~~~~~~~~~~~~~------------~~l~~~~~r~~~~~~~   96 (661)
                      -|.|||+|||+++|| ++|+++| .||  .|.+|.++++..-.-|.+...+.            ..+.++..+..+....
T Consensus         2 s~vv~V~nLp~~~te-~~L~~~f~~fG--~V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~   78 (481)
T TIGR01649         2 SPVVHVRNLPQDVVE-ADLVEALIPFG--PVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQ   78 (481)
T ss_pred             ccEEEEcCCCCCCCH-HHHHHHHHhcC--CeeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCc
Confidence            478999999999999 9999999 999  99999998764222244433322            1112233333332100


Q ss_pred             --------------cCCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHH
Q psy15852         97 --------------EAKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED  161 (661)
Q Consensus        97 --------------~~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~  161 (661)
                                    .....+|++.|++ .+++++|+++|+.||+|.+|.|+++..    +|+|||+|.+.++|.+|    
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~A----  150 (481)
T TIGR01649        79 EIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQHA----  150 (481)
T ss_pred             ccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC----ceEEEEEECCHHHHHHH----
Confidence                          0111256677765 999999999999999999999987542    47999999999999999    


Q ss_pred             HHHhCCeeecce--eehhhhhh----------------------------------------------------------
Q psy15852        162 VIAEGNHVINNK--KIEAKKAK----------------------------------------------------------  181 (661)
Q Consensus       162 ~~~~~~~~i~g~--~i~v~~~~----------------------------------------------------------  181 (661)
                      +..||+..|.+.  .|.|.+++                                                          
T Consensus       151 ~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  230 (481)
T TIGR01649       151 KAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGG  230 (481)
T ss_pred             HHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCC
Confidence            899999988542  23222211                                                          


Q ss_pred             ------------------------------------------ccCCeeEecCCCc-cCCHHHHHHHHhcCCCeEEEEecc
Q psy15852        182 ------------------------------------------AKSGKIFVGGLSP-EMKDEEIKAHFAQFGNIIETEMPY  218 (661)
Q Consensus       182 ------------------------------------------~~~~~lfV~nLp~-~~te~~L~~~F~~~G~i~~v~i~~  218 (661)
                                                                +..++|||+|||+ .+++++|+++|++||.|..|++++
T Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~  310 (481)
T TIGR01649       231 PLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMK  310 (481)
T ss_pred             CCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEe
Confidence                                                      1235899999998 699999999999999999999987


Q ss_pred             CCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCC
Q psy15852        219 DKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKP  264 (661)
Q Consensus       219 ~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~  264 (661)
                      ++     +|||||+|.+.++|.+|+..+ +..|.|++|.|.++..+.
T Consensus       311 ~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~  352 (481)
T TIGR01649       311 NK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQN  352 (481)
T ss_pred             CC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccccc
Confidence            63     799999999999999999987 688999999999986543

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).

>KOG0144|consensus

Probab=100.00  E-value=6.6e-33  Score=277.48  Aligned_cols=165  Identities=24%  Similarity=0.410  Sum_probs=144.3

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCe-eecc--eeeh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH-VINN--KKIE  176 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~-~i~g--~~i~  176 (661)
                      -++||...+..++|.||+++|++||.|.+|.|++|+.|+.++|||||.|.+.++|.+|    +..+++. +|.|  .+|.
T Consensus        35 vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a----~~Alhn~ktlpG~~~pvq  110 (510)
T KOG0144|consen   35 VKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEA----INALHNQKTLPGMHHPVQ  110 (510)
T ss_pred             hhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHH----HHHhhcccccCCCCccee
Confidence            4566666666999999999999999999999999999999999999999999999999    7776554 4544  6777


Q ss_pred             hhhhhcc------CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC--C
Q psy15852        177 AKKAKAK------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK--Q  248 (661)
Q Consensus       177 v~~~~~~------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~--~  248 (661)
                      |++++.+      +++|||+-|++.++|.+++++|++||.|++|.|++|.. +.+||||||+|.+.+-|..||+.++  +
T Consensus       111 vk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~  189 (510)
T KOG0144|consen  111 VKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQ  189 (510)
T ss_pred             ecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHHHHhhccce
Confidence            7777543      46789999999999999999999999999999999987 8999999999999999999999985  4


Q ss_pred             ccCC--eEEEEEeccCCCCCCCC
Q psy15852        249 KIND--KEVDVKKATPKPEPFGV  269 (661)
Q Consensus       249 ~~~g--~~i~V~~a~~k~~~~~~  269 (661)
                      ++.|  .+|.|+||.++.++...
T Consensus       190 tmeGcs~PLVVkFADtqkdk~~~  212 (510)
T KOG0144|consen  190 TMEGCSQPLVVKFADTQKDKDGK  212 (510)
T ss_pred             eeccCCCceEEEecccCCCchHH
Confidence            5665  78999999998876443

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=100.00  E-value=8.2e-32  Score=294.08  Aligned_cols=256  Identities=19%  Similarity=0.239  Sum_probs=194.9

Q ss_pred             hhhHHHhhHHHHHHhCCeeecceeehhhhhh----------ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCC
Q psy15852        151 TESLEKASVEDVIAEGNHVINNKKIEAKKAK----------AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDK  220 (661)
Q Consensus       151 ~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~----------~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~  220 (661)
                      .++|.+|    ++++++..+...........          ...++|||+|||++++|++|+++|++||.|.+|+|++| 
T Consensus        19 ~~~a~~a----~~~~~gy~~~~~~g~r~~g~Pp~~~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-   93 (578)
T TIGR01648        19 DEAALKA----LLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-   93 (578)
T ss_pred             cHHHHHH----HHHhhCccccccCCcccCCCCCCcccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-
Confidence            5777788    77777766654433333321          12389999999999999999999999999999999999 


Q ss_pred             CCCCcCcEEEEEeCCHHHHHHHHHhCC-Ccc-CCeEEEEEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy15852        221 SKSQRKNFCFITFEHESVVIDLLKNPK-QKI-NDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGG  298 (661)
Q Consensus       221 ~~g~~~g~afV~f~~~~~A~~Al~~~~-~~~-~g~~i~V~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~  298 (661)
                      .+++++|||||+|.+.++|++||+.++ ..+ .|+.|.|.++...                                   
T Consensus        94 ~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~~~-----------------------------------  138 (578)
T TIGR01648        94 FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVDN-----------------------------------  138 (578)
T ss_pred             CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccccC-----------------------------------
Confidence            779999999999999999999999974 455 3566555433210                                   


Q ss_pred             CCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhcc
Q psy15852        299 GYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTR  378 (661)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  378 (661)
                                                                                                      
T Consensus       139 --------------------------------------------------------------------------------  138 (578)
T TIGR01648       139 --------------------------------------------------------------------------------  138 (578)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             ccccccccccccccccCCCCCcCccchhhhhhccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCc
Q psy15852        379 SSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQ  458 (661)
Q Consensus       379 ~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~  458 (661)
                                ..++|.++.+.+++++|.+.|..++.                            +.+..+.++.+..+++
T Consensus       139 ----------~rLFVgNLP~~~TeeeL~eeFskv~e----------------------------gvv~vIv~~~~~~kgK  180 (578)
T TIGR01648       139 ----------CRLFVGGIPKNKKREEILEEFSKVTE----------------------------GVVDVIVYHSAADKKK  180 (578)
T ss_pred             ----------ceeEeecCCcchhhHHHHHHhhcccC----------------------------CceEEEEeccccccCc
Confidence                      12344444445899999999988742                            3333344445556678


Q ss_pred             ccceEEEEeCChHHHHHHHhCCC---CcCCCcEEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy15852        459 RKNFCFITFEHESVVIDLLKNPK---QKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG  535 (661)
Q Consensus       459 ~~g~aFV~F~~~e~A~~Ai~~~~---~~l~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~~~  535 (661)
                      ++|||||+|.++++|+.|++...   ..+.|+.|.|.++.+......                                 
T Consensus       181 nRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~---------------------------------  227 (578)
T TIGR01648       181 NRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDE---------------------------------  227 (578)
T ss_pred             cCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccccccc---------------------------------
Confidence            89999999999999999995332   457899999998876522100                                 


Q ss_pred             CCCCccccccccccCCCccccccccccCCCCCcccCCCccccccCCCCccccccccCCCeEEEcCCCCCCCHHHHHHHhh
Q psy15852        536 ELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFS  615 (661)
Q Consensus       536 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~te~dL~~~F~  615 (661)
                                                                          ......++|||+|||+++||++|+++|+
T Consensus       228 ----------------------------------------------------~~~~~~k~LfVgNL~~~~tee~L~~~F~  255 (578)
T TIGR01648       228 ----------------------------------------------------DVMAKVKILYVRNLMTTTTEEIIEKSFS  255 (578)
T ss_pred             ----------------------------------------------------cccccccEEEEeCCCCCCCHHHHHHHHH
Confidence                                                                0011236899999999999999999999


Q ss_pred             cC--CCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        616 KY--GEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       616 ~~--G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      +|  |.|++|++++        |||||+|.+.++|.+|+++++.
T Consensus       256 ~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG  291 (578)
T TIGR01648       256 EFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNG  291 (578)
T ss_pred             hcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCC
Confidence            99  9999998874        5999999999999999997664

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.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.98  E-value=2.2e-30  Score=286.10  Aligned_cols=159  Identities=25%  Similarity=0.404  Sum_probs=143.1

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      ++|++.++++.+++++|+++|++||+|.+|+|+.++.+++++|||||+|.+.++|.+|     +.+++..+.|++|.|..
T Consensus        90 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~A-----l~l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        90 RTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKA-----LALTGQMLLGRPIIVQS  164 (457)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHH-----HHhCCCEECCeeeEEee
Confidence            3455555555999999999999999999999999999999999999999999999996     46999999999998866


Q ss_pred             hhc-----------------cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHH
Q psy15852        180 AKA-----------------KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDL  242 (661)
Q Consensus       180 ~~~-----------------~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A  242 (661)
                      +..                 ..++|||+|||..+++++|+++|++||.|..|.++.+..+|+++|||||+|.+.++|.+|
T Consensus       165 ~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A  244 (457)
T TIGR01622       165 SQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA  244 (457)
T ss_pred             cchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHH
Confidence            421                 137899999999999999999999999999999999999899999999999999999999


Q ss_pred             HHhC-CCccCCeEEEEEeccCC
Q psy15852        243 LKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       243 l~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ++.+ +..|.|+.|.|.++...
T Consensus       245 ~~~l~g~~i~g~~i~v~~a~~~  266 (457)
T TIGR01622       245 LEVMNGFELAGRPIKVGYAQDS  266 (457)
T ss_pred             HHhcCCcEECCEEEEEEEccCC
Confidence            9987 68999999999998843

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.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.97  E-value=2.3e-30  Score=269.98  Aligned_cols=163  Identities=18%  Similarity=0.335  Sum_probs=147.4

Q ss_pred             CCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         99 KNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        99 ~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ..+.|||+++| ++|+++|+++|++||+|++|+|++|+.|+++||||||+|.++++|++|    +..+++..+.+++|.|
T Consensus       106 ~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~A----i~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       106 SGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRA----IKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHH----HHHcCCCccCCceeee
Confidence            44555555555 999999999999999999999999999999999999999999999999    8899999999999999


Q ss_pred             hhhhc-----cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccC
Q psy15852        178 KKAKA-----KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIN  251 (661)
Q Consensus       178 ~~~~~-----~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~  251 (661)
                      .++.+     ...+|||+|||+.+++++|+++|++||+|+.|.|++++.+++++|||||+|.+.++|++||+.+ +..+.
T Consensus       182 ~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~  261 (346)
T TIGR01659       182 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPE  261 (346)
T ss_pred             ecccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccC
Confidence            98764     3478999999999999999999999999999999999999999999999999999999999998 45565


Q ss_pred             C--eEEEEEeccCCCC
Q psy15852        252 D--KEVDVKKATPKPE  265 (661)
Q Consensus       252 g--~~i~V~~a~~k~~  265 (661)
                      +  ++|.|+++..+..
T Consensus       262 g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       262 GGSQPLTVRLAEEHGK  277 (346)
T ss_pred             CCceeEEEEECCcccc
Confidence            5  7999999987544

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).

>KOG0127|consensus

Probab=99.97  E-value=1.8e-31  Score=273.88  Aligned_cols=227  Identities=20%  Similarity=0.312  Sum_probs=191.1

Q ss_pred             ceEEeCCCCCCCCcHHHHHHHh-hhccccccccEEeecCCCCc------eeeecccc----------cccccccccceee
Q psy15852         31 RKLFCPLSSYLELDYLQLWQYF-DWVSSSFSENCLLEDSIGKP------LTVSCSHH----------YYLFDQILRTHFF   93 (661)
Q Consensus        31 r~lfVg~l~~~~te~~~l~~~F-~~g~~~~~~~~~~~d~~~~~------~~~~~~~~----------~~l~~~~~r~~~~   93 (661)
                      .+|||++||++++. ++|.++| +.|  +|..|+++.+..+..      |+|+..+.          +.+..+.++...+
T Consensus         6 ~TlfV~~lp~~~~~-~qL~e~FS~vG--Pik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A   82 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTG-EQLEEFFSYVG--PIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPA   82 (678)
T ss_pred             ceEEEecCCCccch-hHHHHhhhccc--CcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccc
Confidence            78999999999999 9999999 999  999999999977744      66665543          1111111111111


Q ss_pred             e-------------------e----------ecCCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEE
Q psy15852         94 Y-------------------I----------MEAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFA  144 (661)
Q Consensus        94 ~-------------------~----------~~~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~a  144 (661)
                      .                   .          ..++-++||.+||+.+.+.+|+.+|+.||.|.+|.|++.+. |+-+|||
T Consensus        83 ~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFa  161 (678)
T KOG0127|consen   83 KKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFA  161 (678)
T ss_pred             cccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceE
Confidence            0                   0          01134678888888999999999999999999999998766 6666999


Q ss_pred             EEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhhccC----------------------------------------
Q psy15852        145 FIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKAKS----------------------------------------  184 (661)
Q Consensus       145 fV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~~~~----------------------------------------  184 (661)
                      ||+|....+|..|    +..+|++.|.||+|.|.|+.++.                                        
T Consensus       162 FV~fk~~~dA~~A----l~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~  237 (678)
T KOG0127|consen  162 FVQFKEKKDAEKA----LEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEE  237 (678)
T ss_pred             EEEEeeHHHHHHH----HHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhcccc
Confidence            9999999999999    99999999999999999985432                                        


Q ss_pred             -------------------------------------------------------CeeEecCCCccCCHHHHHHHHhcCC
Q psy15852        185 -------------------------------------------------------GKIFVGGLSPEMKDEEIKAHFAQFG  209 (661)
Q Consensus       185 -------------------------------------------------------~~lfV~nLp~~~te~~L~~~F~~~G  209 (661)
                                                                             .+|||+|||+++|+++|.+.|++||
T Consensus       238 d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG  317 (678)
T KOG0127|consen  238 DSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFG  317 (678)
T ss_pred             cccccccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhc
Confidence                                                                   5799999999999999999999999


Q ss_pred             CeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC------C-CccCCeEEEEEeccCCCC
Q psy15852        210 NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP------K-QKINDKEVDVKKATPKPE  265 (661)
Q Consensus       210 ~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~------~-~~~~g~~i~V~~a~~k~~  265 (661)
                      +|..+.|+.++.|++++|.|||.|.+..+|++||..-      + ..++||.|.|..+..+.+
T Consensus       318 ~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~Rke  380 (678)
T KOG0127|consen  318 EVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRKE  380 (678)
T ss_pred             cceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchHH
Confidence            9999999999999999999999999999999999874      3 578999999999988765

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.97  E-value=1.2e-28  Score=269.32  Aligned_cols=162  Identities=20%  Similarity=0.439  Sum_probs=147.1

Q ss_pred             cEEEEcCC-CcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        101 KMVSHPGI-VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       101 ~~~~~~~~-~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +.||++++ +++++++|+++|++||+|.+|+|++|+.||++||||||+|.++++|++|    +..+|+..|.|+.|.|.+
T Consensus       108 ~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~A----i~~lnG~~i~GR~IkV~r  183 (612)
T TIGR01645       108 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLA----LEQMNGQMLGGRNIKVGR  183 (612)
T ss_pred             CEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHH----HHhcCCeEEecceeeecc
Confidence            34555555 4999999999999999999999999999999999999999999999999    889999999999999976


Q ss_pred             hhc----------------cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHH
Q psy15852        180 AKA----------------KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL  243 (661)
Q Consensus       180 ~~~----------------~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al  243 (661)
                      ...                ..++|||+|||+++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|.+|+
T Consensus       184 p~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI  263 (612)
T TIGR01645       184 PSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAI  263 (612)
T ss_pred             cccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHH
Confidence            432                1268999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhC-CCccCCeEEEEEeccCCCCC
Q psy15852        244 KNP-KQKINDKEVDVKKATPKPEP  266 (661)
Q Consensus       244 ~~~-~~~~~g~~i~V~~a~~k~~~  266 (661)
                      +.+ +..++|+.|+|.++..++..
T Consensus       264 ~amNg~elgGr~LrV~kAi~pP~~  287 (612)
T TIGR01645       264 ASMNLFDLGGQYLRVGKCVTPPDA  287 (612)
T ss_pred             HHhCCCeeCCeEEEEEecCCCccc
Confidence            998 57899999999999876543

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.

>KOG0117|consensus

Probab=99.96  E-value=2.2e-28  Score=246.42  Aligned_cols=241  Identities=19%  Similarity=0.282  Sum_probs=193.0

Q ss_pred             CCCCCCCCCCCCC-----CCCceEEeCCCCCCCCcHHHHHHHh-hhccccccccEEeecCCCCc------eeeeccccc-
Q psy15852         15 NGQENGGAPVSVK-----DDDRKLFCPLSSYLELDYLQLWQYF-DWVSSSFSENCLLEDSIGKP------LTVSCSHHY-   81 (661)
Q Consensus        15 ~~~~~~~~~~~~~-----~~~r~lfVg~l~~~~te~~~l~~~F-~~g~~~~~~~~~~~d~~~~~------~~~~~~~~~-   81 (661)
                      +++++=+.|++--     .+--.||||.||.++.| ++|..+| +.|  +|.++.++.|+.+..      |+|...+.. 
T Consensus        63 ~gqrk~ggPpP~weg~~p~~G~EVfvGkIPrD~~E-deLvplfEkiG--~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq  139 (506)
T KOG0117|consen   63 NGQRKYGGPPPGWEGPPPPRGCEVFVGKIPRDVFE-DELVPLFEKIG--KIYELRLMMDPFSGDNRGYAFVTFCTKEEAQ  139 (506)
T ss_pred             ccccccCCCCCcccCCCCCCCceEEecCCCccccc-hhhHHHHHhcc--ceeeEEEeecccCCCCcceEEEEeecHHHHH
Confidence            4555555554432     24467999999999999 9999999 999  999999999965554      776665541 


Q ss_pred             ----cccccccc---ceeeeeecCCCcEEEEcCCCcCCHHHHHHHhhcCCC-eeEEEEeeCCC-CCCcccEEEEEEeehh
Q psy15852         82 ----YLFDQILR---THFFYIMEAKNKMVSHPGIVHKITEELKEHFSKYGE-IENVTLKSDPN-TGRSRGFAFIVFKDTE  152 (661)
Q Consensus        82 ----~l~~~~~r---~~~~~~~~~~~~~~~~~~~~~~te~~L~~~F~~~G~-I~~v~l~~~~~-tg~srG~afV~F~~~e  152 (661)
                          .|.+..+|   ...+-....+.+||+.+.|.++++++|.+.|++.++ |++|.|..++. ..++||||||+|.++.
T Consensus       140 ~Aik~lnn~Eir~GK~igvc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~  219 (506)
T KOG0117|consen  140 EAIKELNNYEIRPGKLLGVCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHR  219 (506)
T ss_pred             HHHHHhhCccccCCCEeEEEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecch
Confidence                22222222   223334556667777666669999999999999999 99999988765 3579999999999999


Q ss_pred             hHHHhhHHHHHHhCCeeecceeehhhhhhccC----------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCC
Q psy15852        153 SLEKASVEDVIAEGNHVINNKKIEAKKAKAKS----------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSK  222 (661)
Q Consensus       153 ~A~~A~~~~~~~~~~~~i~g~~i~v~~~~~~~----------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~  222 (661)
                      .|..|  ++.+.-....++|..+.|.|+.+..          +-|||+||+.++|++.|+++|++||.|+.|+.+     
T Consensus       220 ~Aa~a--RrKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~-----  292 (506)
T KOG0117|consen  220 AAAMA--RRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKP-----  292 (506)
T ss_pred             hHHHH--HhhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecc-----
Confidence            99887  2223335567899999999998765          789999999999999999999999999999876     


Q ss_pred             CCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCCCCCC
Q psy15852        223 SQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKPEPFG  268 (661)
Q Consensus       223 g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~~~~~  268 (661)
                         +.||||+|.+.++|.+||+.+ +..|+|..|.|.+|+|..+..-
T Consensus       293 ---rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k~  336 (506)
T KOG0117|consen  293 ---RDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKKK  336 (506)
T ss_pred             ---cceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhcc
Confidence               449999999999999999998 5899999999999999776543

>KOG0123|consensus

Probab=99.96  E-value=7.8e-29  Score=259.60  Aligned_cols=317  Identities=21%  Similarity=0.276  Sum_probs=243.5

Q ss_pred             eEEeCCCCCCCCcHHHHHHHh-hhccccccccEEeecCCCCceeeecccc---------------cccccccccceeeee
Q psy15852         32 KLFCPLSSYLELDYLQLWQYF-DWVSSSFSENCLLEDSIGKPLTVSCSHH---------------YYLFDQILRTHFFYI   95 (661)
Q Consensus        32 ~lfVg~l~~~~te~~~l~~~F-~~g~~~~~~~~~~~d~~~~~~~~~~~~~---------------~~l~~~~~r~~~~~~   95 (661)
                      .||||   +++|| .+|.++| .+|  ++.++.+++|. + .+.++-...               ..+.++..|+.|...
T Consensus         3 sl~vg---~~v~e-~~l~~~f~~~~--~v~s~rvc~d~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~r   74 (369)
T KOG0123|consen    3 SLYVG---PDVTE-AMLFDKFSPAG--PVLSIRVCRDA-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQR   74 (369)
T ss_pred             ceecC---CcCCh-HHHHHHhcccC--CceeEEEeecC-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhcc
Confidence            58999   99999 9999999 999  99999999998 7 754444333               223345566666533


Q ss_pred             ecCCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeeccee
Q psy15852         96 MEAKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK  174 (661)
Q Consensus        96 ~~~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~  174 (661)
                      .+   .++++.|++ +++..+|.++|+.||+|++|+|..+.+ | ++|| ||+|+++++|.+|    +..+|+..+.+++
T Consensus        75 d~---~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~a----i~~~ng~ll~~kk  144 (369)
T KOG0123|consen   75 DP---SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKA----IEKLNGMLLNGKK  144 (369)
T ss_pred             CC---ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHH----HHHhcCcccCCCe
Confidence            32   236666665 999999999999999999999999876 5 9999 9999999999999    9999999999999


Q ss_pred             ehhhhhhccC-------------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHH
Q psy15852        175 IEAKKAKAKS-------------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVID  241 (661)
Q Consensus       175 i~v~~~~~~~-------------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~  241 (661)
                      |.|.....+.             ..++|.|++.+++++.|.++|+.+|.|.++.++.+.. +++++|+||.|.++++|.+
T Consensus       145 i~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~-g~~~~~gfv~f~~~e~a~~  223 (369)
T KOG0123|consen  145 IYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSI-GKSKGFGFVNFENPEDAKK  223 (369)
T ss_pred             eEEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCC-CCCCCccceeecChhHHHH
Confidence            9986654322             5789999999999999999999999999999999875 6699999999999999999


Q ss_pred             HHHhCC-CccCCeEEEEEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCC
Q psy15852        242 LLKNPK-QKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISG  320 (661)
Q Consensus       242 Al~~~~-~~~~g~~i~V~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~  320 (661)
                      |++.++ ..+.+..+.|..+..+.+...                                                    
T Consensus       224 av~~l~~~~~~~~~~~V~~aqkk~e~~~----------------------------------------------------  251 (369)
T KOG0123|consen  224 AVETLNGKIFGDKELYVGRAQKKSEREA----------------------------------------------------  251 (369)
T ss_pred             HHHhccCCcCCccceeecccccchhhHH----------------------------------------------------
Confidence            999984 567788888888776433200                                                    


Q ss_pred             CCCCCCCCCCCCCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccc-cccccccCCCCC
Q psy15852        321 RSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHV-ADNLLLCDNFPS  399 (661)
Q Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~-~~~~~~~~~~p~  399 (661)
                                                                        .++.-|....-...-.+ .-++++.+....
T Consensus       252 --------------------------------------------------~l~~~~~~~~~~~~~~~~~~nl~vknld~~  281 (369)
T KOG0123|consen  252 --------------------------------------------------ELKRKFEQEFAKRSVSLQGANLYVKNLDET  281 (369)
T ss_pred             --------------------------------------------------HHhhhhHhhhhhccccccccccccccCccc
Confidence                                                              00000000000000000 112333334445


Q ss_pred             cCccchhhhhhccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHH-h
Q psy15852        400 IRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL-K  478 (661)
Q Consensus       400 ~~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai-~  478 (661)
                      ++.+.++..|..+                              |+|.++++..+ ..++++||+||.|.++++|.+|+ .
T Consensus       282 ~~~e~L~~~f~~~------------------------------GeI~s~kv~~~-~~g~skG~gfV~fs~~eeA~~A~~~  330 (369)
T KOG0123|consen  282 LSDEKLRKIFSSF------------------------------GEITSAKVMVD-ENGKSKGFGFVEFSSPEEAKKAMTE  330 (369)
T ss_pred             cchhHHHHHHhcc------------------------------cceeeEEEEec-cCCCccceEEEEcCCHHHHHHHHHh
Confidence            8888888888887                              78999888775 45788999999999999999999 4


Q ss_pred             CCCCcCCCcEEEEecCCCCCCC
Q psy15852        479 NPKQKINDKEVDVKKATPKPEP  500 (661)
Q Consensus       479 ~~~~~l~g~~i~v~~a~~~~~~  500 (661)
                      .++..+.++.|.|.++..+..+
T Consensus       331 ~n~~~i~~k~l~vav~qr~~~r  352 (369)
T KOG0123|consen  331 MNGRLIGGKPLYVAVAQRKEDR  352 (369)
T ss_pred             hChhhhcCCchhhhHHhhhccc
Confidence            5557788899988887755443

>KOG0148|consensus

Probab=99.96  E-value=3.6e-28  Score=230.14  Aligned_cols=233  Identities=16%  Similarity=0.276  Sum_probs=177.8

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      -+++||+|+. ++||+-|..||++.|+|+.++|+.+.-                ....|    ..--+...         
T Consensus         6 prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~----------------~v~wa----~~p~nQsk---------   56 (321)
T KOG0148|consen    6 PRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDEL----------------KVNWA----TAPGNQSK---------   56 (321)
T ss_pred             CceEEeeccChhhHHHHHHHHHHhccccccceeehhhh----------------ccccc----cCcccCCC---------
Confidence            3455666655 999999999999999999999998721                11111    00000000         


Q ss_pred             hhhccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEE
Q psy15852        179 KAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDV  257 (661)
Q Consensus       179 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V  257 (661)
                      ......-.+||+.|...++.++|++.|.+||+|.+++|++|..|+++|||+||.|-+.++|+.||..| ++.|.+|.|+-
T Consensus        57 ~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRT  136 (321)
T KOG0148|consen   57 PTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRT  136 (321)
T ss_pred             CccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeec
Confidence            00111236999999999999999999999999999999999999999999999999999999999998 58899999999


Q ss_pred             EeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCC
Q psy15852        258 KKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPL  337 (661)
Q Consensus       258 ~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  337 (661)
                      .||..|+......                                                               .   
T Consensus       137 NWATRKp~e~n~~---------------------------------------------------------------~---  150 (321)
T KOG0148|consen  137 NWATRKPSEMNGK---------------------------------------------------------------P---  150 (321)
T ss_pred             cccccCccccCCC---------------------------------------------------------------C---
Confidence            9999887321000                                                               0   


Q ss_pred             cccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCC-cCccchhhhhhccCccc
Q psy15852        338 AEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPS-IRELEIPEAFLTKTTTV  416 (661)
Q Consensus       338 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~-~~~~~l~~~f~~~~~~~  416 (661)
                                                   .+-+++   |.+      ..-.++-++|.+.+. +++++++..|++|    
T Consensus       151 -----------------------------ltfdeV---~NQ------ssp~NtsVY~G~I~~~lte~~mr~~Fs~f----  188 (321)
T KOG0148|consen  151 -----------------------------LTFDEV---YNQ------SSPDNTSVYVGNIASGLTEDLMRQTFSPF----  188 (321)
T ss_pred             -----------------------------ccHHHH---hcc------CCCCCceEEeCCcCccccHHHHHHhcccC----
Confidence                                         000111   100      012456678888888 9999999999998    


Q ss_pred             ccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHH-hCCCCcCCCcEEEEecCC
Q psy15852        417 PMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL-KNPKQKINDKEVDVKKAT  495 (661)
Q Consensus       417 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai-~~~~~~l~g~~i~v~~a~  495 (661)
                                                |.|.+|++..+      +||+||.|++.|+|.+|| ..++.+++|..+++.|.+
T Consensus       189 --------------------------G~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGK  236 (321)
T KOG0148|consen  189 --------------------------GPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGK  236 (321)
T ss_pred             --------------------------CcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccc
Confidence                                      66999998764      699999999999999999 566689999999999988


Q ss_pred             CCCCCC
Q psy15852        496 PKPEPF  501 (661)
Q Consensus       496 ~~~~~~  501 (661)
                      ......
T Consensus       237 e~~~~~  242 (321)
T KOG0148|consen  237 EGDDGI  242 (321)
T ss_pred             cCCCCC
Confidence            765443

>KOG0110|consensus

Probab=99.96  E-value=3.4e-28  Score=258.37  Aligned_cols=349  Identities=16%  Similarity=0.205  Sum_probs=235.9

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ...++|+.+|++.++++||+.+|                       +||.|..++.|.+|    -..++++.+.|+-+.|
T Consensus       226 etgrlf~RNLpyt~~eed~~~lf-----------------------a~v~~~~~~~avka----~~~~D~k~fqgrmlhv  278 (725)
T KOG0110|consen  226 ETGRLFVRNLPYTSTEEDLLKLF-----------------------AFVTFMFPEHAVKA----YSELDGKVFQGRMLHV  278 (725)
T ss_pred             hhhhhhhccCCccccHHHHHHhh-----------------------HHHhhhhhHHHHhh----hhhccccccccceeee
Confidence            45678888888899999999999                       88889999999998    8888899888888876


Q ss_pred             hhhhccC-------------------------------------------------------------------------
Q psy15852        178 KKAKAKS-------------------------------------------------------------------------  184 (661)
Q Consensus       178 ~~~~~~~-------------------------------------------------------------------------  184 (661)
                      .+..++.                                                                         
T Consensus       279 lp~~~k~~~~~~~~~~~~~~k~~ke~~rk~~~~~~~~wn~l~~~~~ava~~~a~k~~v~k~~i~d~~~~gsavr~al~et  358 (725)
T KOG0110|consen  279 LPSKEKSTAKEDASELGSDYKKEKELKRKAASASFHSWNTLFMGANAVAGILAQKLGVEKSRILDGSLSGSAVRLALGET  358 (725)
T ss_pred             cCcchhhhhhhhHhhcCCcHHHHHHhccccchhcceecccccccccHHHHHHHHHhCCeeeeeechhhcchHHHHHHHHh
Confidence            5433211                                                                         


Q ss_pred             ---------------------------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHH
Q psy15852        185 ---------------------------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES  237 (661)
Q Consensus       185 ---------------------------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~  237 (661)
                                                 +.|+|+|||..+..++|...|..||+|..+.++..      --.|+|+|.++.
T Consensus       359 r~~~e~~~~~ee~gV~l~~F~~~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~------G~~aiv~fl~p~  432 (725)
T KOG0110|consen  359 RVVQEVRRFFEENGVKLDAFSQAERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPG------GTGAIVEFLNPL  432 (725)
T ss_pred             hhchhhhhhHHhhCcccccchhhhhhcceeeeccCccccccHHHHHHhhcccccceeecCcc------cceeeeeecCcc
Confidence                                       45999999999999999999999999999966521      223999999999


Q ss_pred             HHHHHHHhCC-CccCCeEEEEEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccC
Q psy15852        238 VVIDLLKNPK-QKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNEL  316 (661)
Q Consensus       238 ~A~~Al~~~~-~~~~g~~i~V~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~  316 (661)
                      +|.+|++.+. ..+...++.+.|+...-..-                                      .|...      
T Consensus       433 eAr~Afrklaysr~k~~plyle~aP~dvf~~--------------------------------------~pka~------  468 (725)
T KOG0110|consen  433 EARKAFRKLAYSRFKSAPLYLEWAPEDVFTE--------------------------------------DPKAD------  468 (725)
T ss_pred             chHHHHHHhchhhhccCccccccChhhhccC--------------------------------------Ccccc------
Confidence            9999999984 56777777777765422110                                      00000      


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCC
Q psy15852        317 GISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDN  396 (661)
Q Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  396 (661)
                             ...+.+.    .++.+..     .-.+........+..++.+..+...+-.-.          ...+.|+..|
T Consensus       469 -------~~~~e~~----~~~ee~~-----~Er~s~~d~~v~eD~d~te~ss~a~~a~~~----------~~~t~lfvkN  522 (725)
T KOG0110|consen  469 -------DLSAESR----SKMEENP-----SERVSAEDGQVEEDKDPTEESSLARVAEDE----------ETETKLFVKN  522 (725)
T ss_pred             -------ccccccc----cccccCc-----ceecccccccccccCCccccccchhhhhcc----------ccchhhhhhc
Confidence                   0000000    0000000     000000000000000000011101010000          0111133334


Q ss_pred             CCC-cCccchhhhhhccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccC---CcccceEEEEeCChHH
Q psy15852        397 FPS-IRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSK---SQRKNFCFITFEHESV  472 (661)
Q Consensus       397 ~p~-~~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~---~~~~g~aFV~F~~~e~  472 (661)
                      ++. ++.+++..+|...                              |.|.++.|...+..   -.++|||||+|.++++
T Consensus       523 lnf~Tt~e~l~~~F~k~------------------------------G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~  572 (725)
T KOG0110|consen  523 LNFDTTLEDLEDLFSKQ------------------------------GTVLSIEISKKKDPANKYLSMGFGFVEFAKPES  572 (725)
T ss_pred             CCcccchhHHHHHHHhc------------------------------CeEEEEEEeccccccccccccceeEEEecCHHH
Confidence            443 7777777777665                              78999987654432   3467999999999999


Q ss_pred             HHHHHhCCC-CcCCCcEEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCC
Q psy15852        473 VIDLLKNPK-QKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISS  551 (661)
Q Consensus       473 A~~Ai~~~~-~~l~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~~~~~~~~~~~~~~~~~~~  551 (661)
                      |+.|+..++ ..|+|+.|.|+.+..++....+                                                
T Consensus       573 A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~g------------------------------------------------  604 (725)
T KOG0110|consen  573 AQAALKALQGTVLDGHKLELKISENKPASTVG------------------------------------------------  604 (725)
T ss_pred             HHHHHHHhcCceecCceEEEEeccCccccccc------------------------------------------------
Confidence            999998766 8899999999888733221100                                                


Q ss_pred             CccccccccccCCCCCcccCCCccccccCCCCccccccccCCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCC
Q psy15852        552 SFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNT  631 (661)
Q Consensus       552 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~t  631 (661)
                                    +                   ..+.....++|+|+||||+++..+|+++|++||+|.+|+||.....
T Consensus       605 --------------K-------------------~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k  651 (725)
T KOG0110|consen  605 --------------K-------------------KKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGK  651 (725)
T ss_pred             --------------c-------------------ccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcc
Confidence                          0                   0001112579999999999999999999999999999999998667


Q ss_pred             CCcccEEEEEEcCHHHHHHHHHh--CCcccC
Q psy15852        632 GRSRGFAFIVFKDTESLEKASVE--DVYFYS  660 (661)
Q Consensus       632 g~s~G~aFV~F~~~e~A~~A~~~--~~~~~~  660 (661)
                      +.++|||||+|.++.+|.+|++.  .+|||-
T Consensus       652 ~a~rGF~Fv~f~t~~ea~nA~~al~STHlyG  682 (725)
T KOG0110|consen  652 GAHRGFGFVDFLTPREAKNAFDALGSTHLYG  682 (725)
T ss_pred             hhhccceeeeccCcHHHHHHHHhhcccceec
Confidence            88899999999999999999986  678873

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.95  E-value=1.2e-26  Score=260.10  Aligned_cols=153  Identities=18%  Similarity=0.362  Sum_probs=129.5

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcC------------CCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhC
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKY------------GEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEG  166 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~------------G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~  166 (661)
                      .+.|||+|+| ++|+++|+++|.+|            +.|..+.+      ++++|||||+|.+.++|.+|    + .++
T Consensus       175 ~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~A----l-~l~  243 (509)
T TIGR01642       175 ARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFA----M-ALD  243 (509)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhh----h-cCC
Confidence            3445555555 99999999999985            23444444      34678999999999999997    5 799


Q ss_pred             Ceeecceeehhhhhh----------------------------------ccCCeeEecCCCccCCHHHHHHHHhcCCCeE
Q psy15852        167 NHVINNKKIEAKKAK----------------------------------AKSGKIFVGGLSPEMKDEEIKAHFAQFGNII  212 (661)
Q Consensus       167 ~~~i~g~~i~v~~~~----------------------------------~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~  212 (661)
                      +..+.|+.|.|....                                  ...++|||+|||..+++++|+++|++||.|.
T Consensus       244 g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~  323 (509)
T TIGR01642       244 SIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLK  323 (509)
T ss_pred             CeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCee
Confidence            999999999886421                                  1126899999999999999999999999999


Q ss_pred             EEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        213 ETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       213 ~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      .+.|+.+..+|.++|||||+|.+.++|.+||+.+ +..|.|+.|.|.++...
T Consensus       324 ~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       324 AFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             EEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence            9999999989999999999999999999999987 68999999999998753

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.95  E-value=2.1e-26  Score=258.04  Aligned_cols=289  Identities=17%  Similarity=0.200  Sum_probs=188.7

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcC------------CCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCc
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQF------------GNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQK  249 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~------------G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~  249 (661)
                      ...++|||+|||+.+++++|+++|.++            +.|..+.+      ++.+|||||+|.+.++|.+||+..+..
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~l~g~~  246 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMALDSII  246 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhcCCCeE
Confidence            345899999999999999999999875            34555555      345899999999999999999766889


Q ss_pred             cCCeEEEEEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCC
Q psy15852        250 INDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGP  329 (661)
Q Consensus       250 ~~g~~i~V~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  329 (661)
                      |.|+.|.|.............                                                          +
T Consensus       247 ~~g~~l~v~r~~~~~~~~~~~----------------------------------------------------------~  268 (509)
T TIGR01642       247 YSNVFLKIRRPHDYIPVPQIT----------------------------------------------------------P  268 (509)
T ss_pred             eeCceeEecCccccCCccccC----------------------------------------------------------C
Confidence            999999997543321100000                                                          0


Q ss_pred             CCCCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhh
Q psy15852        330 MVQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAF  409 (661)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f  409 (661)
                      ......+...  .        .....  .....    .                ...-...|+|.++...+++++|+++|
T Consensus       269 ~~~~~~~~~~--~--------~~~~~--~~~~~----~----------------~~~~~~~l~v~nlp~~~~~~~l~~~f  316 (509)
T TIGR01642       269 EVSQKNPDDN--A--------KNVEK--LVNST----T----------------VLDSKDRIYIGNLPLYLGEDQIKELL  316 (509)
T ss_pred             CCCCCCCccc--c--------ccccc--ccccc----c----------------CCCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            0000000000  0        00000  00000    0                00011235555554459999999999


Q ss_pred             hccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHH-hCCCCcCCCcE
Q psy15852        410 LTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL-KNPKQKINDKE  488 (661)
Q Consensus       410 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai-~~~~~~l~g~~  488 (661)
                      ..|                              |.|..+.++.+..+++++|||||+|.+.++|..|| .+++..+.|+.
T Consensus       317 ~~~------------------------------G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~  366 (509)
T TIGR01642       317 ESF------------------------------GDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNK  366 (509)
T ss_pred             Hhc------------------------------CCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeE
Confidence            988                              67999999999999999999999999999999999 56778899999


Q ss_pred             EEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCccccccccccCCCCCc
Q psy15852        489 VDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLT  568 (661)
Q Consensus       489 i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~  568 (661)
                      |.|.++............                              .+                         ..|..
T Consensus       367 l~v~~a~~~~~~~~~~~~------------------------------~~-------------------------~~~~~  391 (509)
T TIGR01642       367 LHVQRACVGANQATIDTS------------------------------NG-------------------------MAPVT  391 (509)
T ss_pred             EEEEECccCCCCCCcccc------------------------------cc-------------------------ccccc
Confidence            999988754221100000                              00                         00000


Q ss_pred             ccCCCccccccCCCCccccccccCCCeEEEcCCCCCC----------CHHHHHHHhhcCCCeeEEEEeec---CCCCCcc
Q psy15852        569 VSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDK----------ITEELKEHFSKYGEIENVTLKSD---PNTGRSR  635 (661)
Q Consensus       569 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~----------te~dL~~~F~~~G~I~~v~i~~d---~~tg~s~  635 (661)
                      .........       ...........|++.|+++..          ..++|+++|++||.|++|+|+++   ..++.+.
T Consensus       392 ~~~~~~~~~-------~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~  464 (509)
T TIGR01642       392 LLAKALSQS-------ILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGV  464 (509)
T ss_pred             cccccchhh-------hccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCc
Confidence            000000000       000001124678999997521          23689999999999999999975   3346778


Q ss_pred             cEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        636 GFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       636 G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      |+|||+|.++++|.+|+..+|..
T Consensus       465 G~~fV~F~~~e~A~~A~~~lnGr  487 (509)
T TIGR01642       465 GKVFLEYADVRSAEKAMEGMNGR  487 (509)
T ss_pred             ceEEEEECCHHHHHHHHHHcCCC
Confidence            99999999999999999998753

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0145|consensus

Probab=99.95  E-value=7.9e-27  Score=219.24  Aligned_cols=228  Identities=21%  Similarity=0.258  Sum_probs=187.7

Q ss_pred             CCceEEeCCCCCCCCcHHHHHHHh-hhccccccccEEeecCCCCc------eeeecccc----------cccccccccce
Q psy15852         29 DDRKLFCPLSSYLELDYLQLWQYF-DWVSSSFSENCLLEDSIGKP------LTVSCSHH----------YYLFDQILRTH   91 (661)
Q Consensus        29 ~~r~lfVg~l~~~~te~~~l~~~F-~~g~~~~~~~~~~~d~~~~~------~~~~~~~~----------~~l~~~~~r~~   91 (661)
                      ....|.|--||..+|+ |.|+.+| ..|  +|.+|+++||..+.+      |.+...+.          .+|-...++.+
T Consensus        40 skTNLIvNYLPQ~MTq-dE~rSLF~SiG--eiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQ-DELRSLFGSIG--EIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             ccceeeeeecccccCH-HHHHHHhhccc--ceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            3456999999999999 9999999 999  999999999987776      33333222          12222223333


Q ss_pred             eeeee--cCCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCe
Q psy15852         92 FFYIM--EAKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH  168 (661)
Q Consensus        92 ~~~~~--~~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~  168 (661)
                      ++...  .-+...+|+..+| .+|..||+++|++||.|..-+|..|..||.+||.+||.|+..++|+.|    |..+||+
T Consensus       117 yARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~A----Ik~lNG~  192 (360)
T KOG0145|consen  117 YARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEA----IKGLNGQ  192 (360)
T ss_pred             eccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHH----HHhccCC
Confidence            32211  1245567777777 999999999999999999999999999999999999999999999999    9999998


Q ss_pred             eecc--eeehhhhhhccC--------------------------------------------------------------
Q psy15852        169 VINN--KKIEAKKAKAKS--------------------------------------------------------------  184 (661)
Q Consensus       169 ~i~g--~~i~v~~~~~~~--------------------------------------------------------------  184 (661)
                      .-.|  .+|.|+++..++                                                              
T Consensus       193 ~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp  272 (360)
T KOG0145|consen  193 KPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLP  272 (360)
T ss_pred             CCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccC
Confidence            7655  345555443221                                                              


Q ss_pred             ------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEE
Q psy15852        185 ------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDV  257 (661)
Q Consensus       185 ------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V  257 (661)
                            .+|||-||.++++|.-|+++|.+||.|..|++++|..|.++|||+||...+.++|..||..+ +..+.+|.|.|
T Consensus       273 ~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQV  352 (360)
T KOG0145|consen  273 GGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQV  352 (360)
T ss_pred             CCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEE
Confidence                  68999999999999999999999999999999999999999999999999999999999998 57899999999


Q ss_pred             EeccCC
Q psy15852        258 KKATPK  263 (661)
Q Consensus       258 ~~a~~k  263 (661)
                      .+...+
T Consensus       353 sFKtnk  358 (360)
T KOG0145|consen  353 SFKTNK  358 (360)
T ss_pred             EEecCC
Confidence            987665

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.94  E-value=5.3e-26  Score=237.25  Aligned_cols=170  Identities=18%  Similarity=0.249  Sum_probs=143.2

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+++++++|+++|++||+|++|+|++|..+++++|||||+|.++++|++||+.+ +..+.+++|+|.++
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a  184 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA  184 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence            34589999999999999999999999999999999999999999999999999999999999887 68899999999987


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCccc
Q psy15852        261 TPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEV  340 (661)
Q Consensus       261 ~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (661)
                      .+....                                                                          
T Consensus       185 ~p~~~~--------------------------------------------------------------------------  190 (346)
T TIGR01659       185 RPGGES--------------------------------------------------------------------------  190 (346)
T ss_pred             cccccc--------------------------------------------------------------------------
Confidence            642210                                                                          


Q ss_pred             CCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCC
Q psy15852        341 DVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTT  420 (661)
Q Consensus       341 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~  420 (661)
                                                                   .-...|+|.++.+.+++++|+++|..|        
T Consensus       191 ---------------------------------------------~~~~~lfV~nLp~~vtee~L~~~F~~f--------  217 (346)
T TIGR01659       191 ---------------------------------------------IKDTNLYVTNLPRTITDDQLDTIFGKY--------  217 (346)
T ss_pred             ---------------------------------------------cccceeEEeCCCCcccHHHHHHHHHhc--------
Confidence                                                         000124455555559999999999888        


Q ss_pred             cccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHh-CCCCcCCC--cEEEEecCCCC
Q psy15852        421 TEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK-NPKQKIND--KEVDVKKATPK  497 (661)
Q Consensus       421 ~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~-~~~~~l~g--~~i~v~~a~~~  497 (661)
                                            |+|+.+.++.|+.+++++|||||+|.+.++|++||+ +++..+.+  +.|.|+++...
T Consensus       218 ----------------------G~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       218 ----------------------GQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             ----------------------CCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcc
Confidence                                  789999999999999999999999999999999995 55565655  68899888766


Q ss_pred             CCC
Q psy15852        498 PEP  500 (661)
Q Consensus       498 ~~~  500 (661)
                      ...
T Consensus       276 ~~~  278 (346)
T TIGR01659       276 GKA  278 (346)
T ss_pred             ccc
Confidence            443

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).

>KOG4211|consensus

Probab=99.94  E-value=8.3e-24  Score=216.74  Aligned_cols=443  Identities=17%  Similarity=0.189  Sum_probs=246.0

Q ss_pred             EEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhhc
Q psy15852        103 VSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKA  182 (661)
Q Consensus       103 ~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~~  182 (661)
                      =..+||+++|++||.++|+.++ |+++.+.+.  +|+..|-|||+|.++|++++|     ++.+...+..+.|.|-.+..
T Consensus        14 r~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~A-----lkkdR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen   14 RLRGLPWSATEKEILDFFSNCG-IENLEIPRR--NGRPSGEAYVEFTSEEDVEKA-----LKKDRESMGHRYIEVFTAGG   85 (510)
T ss_pred             EecCCCccccHHHHHHHHhcCc-eeEEEEecc--CCCcCcceEEEeechHHHHHH-----HHhhHHHhCCceEEEEccCC
Confidence            3567778999999999999995 778777663  699999999999999999996     55556666666676655422


Q ss_pred             c----------------CCeeEecCCCccCCHHHHHHHHhcCCCeEE-EEeccCCCCCCcCcEEEEEeCCHHHHHHHHHh
Q psy15852        183 K----------------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIE-TEMPYDKSKSQRKNFCFITFEHESVVIDLLKN  245 (661)
Q Consensus       183 ~----------------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~-v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~  245 (661)
                      .                .-.|.+++||+.|+++||.++|+..-.|.. |.++.+.. +++.|-|||+|++.+.|++||..
T Consensus        86 ~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~r-gR~tGEAfVqF~sqe~ae~Al~r  164 (510)
T KOG4211|consen   86 AEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQR-GRPTGEAFVQFESQESAEIALGR  164 (510)
T ss_pred             ccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCC-CCcccceEEEecCHHHHHHHHHH
Confidence            1                246899999999999999999998776655 44555544 78999999999999999999999


Q ss_pred             CCCccCCeEEEEEeccCCCCCCCC-----CCCCC----C-CCCCCCCC-CCCCCCCC---CCCCCCCCCCCCCCCCcccc
Q psy15852        246 PKQKINDKEVDVKKATPKPEPFGV-----RGGRG----G-RGGRGGRG-GRMAGGYG---GYGGYGGGYGGILYKPLLFY  311 (661)
Q Consensus       246 ~~~~~~g~~i~V~~a~~k~~~~~~-----~~~~~----~-~g~~~g~~-~~~~~~~g---~~~g~~~~~~~~~~~~~~~~  311 (661)
                      ....|.-|-|+|-.+.....+..-     ..++.    . .+.+++.. +...+...   .++.+.+++  .++.+....
T Consensus       165 hre~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~--~g~~~~~~~  242 (510)
T KOG4211|consen  165 HRENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGY--YGFSRYPSL  242 (510)
T ss_pred             HHHhhccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCc--cccccCccc
Confidence            988899999999776543322110     00000    0 00111100 00000000   001111111  111111111


Q ss_pred             ccccCCCCCCCCCCCCCCCCCCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccc
Q psy15852        312 ELNELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNL  391 (661)
Q Consensus       312 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  391 (661)
                      .. ....... ...+...+.....  .+...                                  ....+..++....+.
T Consensus       243 ~d-~~~~gs~-~~~~~~~~~~~~g--~~~~g----------------------------------~~g~~~~~~~~g~fv  284 (510)
T KOG4211|consen  243 QD-YGNFGSY-GGGRDPNYPVSSG--PHRQG----------------------------------GAGDYGNGGPGGHFV  284 (510)
T ss_pred             cc-ccccccc-ccccccccCCCCC--cccCC----------------------------------CcccccCCCCCCcee
Confidence            00 0000000 0000000000000  00000                                  000111122222222


Q ss_pred             cccCCCCCcCccchhhhhhccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChH
Q psy15852        392 LLCDNFPSIRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHES  471 (661)
Q Consensus       392 ~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e  471 (661)
                      -+..+.-..++.++..+|++..|                               ..+.+-.. .+++..|-|+|.|.+.+
T Consensus       285 ~MRGlpy~a~~~di~nfFspl~p-------------------------------~~v~i~ig-~dGr~TGEAdveF~t~e  332 (510)
T KOG4211|consen  285 HMRGLPYDATENDIANFFSPLNP-------------------------------YRVHIEIG-PDGRATGEADVEFATGE  332 (510)
T ss_pred             eecCCCccCCCcchhhhcCCCCc-------------------------------eeEEEEeC-CCCccCCcceeecccch
Confidence            23333333778888888887643                               45554442 45777899999999999


Q ss_pred             HHHHHHhCCCCcCCCcEEEEecCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCC-CCCCCCCCCCcccccccc
Q psy15852        472 VVIDLLKNPKQKINDKEVDVKKATPKPEPFGVRGGRGGR---GGRGGRGGRMAGGYGGYGG-YGGGYGELDYLQLWQFFD  547 (661)
Q Consensus       472 ~A~~Ai~~~~~~l~g~~i~v~~a~~~~~~~~~~~~~~~~---~~~~~~~~~~~~g~gg~~~-~g~~~~~~~~~~~~~~~~  547 (661)
                      +|..||...+..+..+.|++-.-.....+.+..+...+.   .+..+.+|.+.+  +.+.+ ++++.+...+.++++.. 
T Consensus       333 dav~Amskd~anm~hrYVElFln~~~ga~g~~~~s~~~g~~~~~~~~~~Gg~a~--g~~~gG~~g~~~~~~~~G~~~~~-  409 (510)
T KOG4211|consen  333 DAVGAMGKDGANMGHRYVELFLNGAPGASGGGGPSGPGGVGSSGDRNGGGGYAS--GSYGGGGNGGGGRGSPYGRPSDG-  409 (510)
T ss_pred             hhHhhhccCCcccCcceeeecccCCcccccCccCCCCCCccccccccCCCCccc--cccccCCCCCccccCCCCCCccc-
Confidence            999999888888999988875543221111110000000   000000111000  11111 11111111111111111 


Q ss_pred             ccCCCccccccccccCCCCCcccCCCccccccCCCCccccccccCCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEee
Q psy15852        548 WISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKS  627 (661)
Q Consensus       548 ~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~  627 (661)
                      ..+.....       ...|..  ....+              ....-.|-.+.+|+-.++.|+.++|.++++- .|.|.+
T Consensus       410 ~~~~~~~G-------y~g~~~--~~~~~--------------~~e~~~~~~rgap~~a~eadv~d~~~~~~~a-~~~~~y  465 (510)
T KOG4211|consen  410 YSSPGGGG-------YSGPRG--YGRGP--------------QNEHFVIRMRGAPFRASEADVYDFFHPIRPA-QVELLY  465 (510)
T ss_pred             ccCCCCCC-------CcCccc--CCCCc--------------cccccccCcCCCCccccccchhhcccccCcc-cccccc
Confidence            11111000       000000  00000              0112356678899999999999999999876 899999


Q ss_pred             cCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        628 DPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       628 d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      |+. ....|-|-|.|.+.++++.|+.+
T Consensus       466 d~~-~~~~~~a~~~~~~~~~~q~a~~~  491 (510)
T KOG4211|consen  466 DHQ-FQRSGDARVIFYNRKDYQDALMK  491 (510)
T ss_pred             ccc-ccccCceeEEEechhhhHHHHHh
Confidence            998 55599999999999999999986

>KOG0144|consensus

Probab=99.93  E-value=1.2e-25  Score=225.60  Aligned_cols=229  Identities=22%  Similarity=0.320  Sum_probs=191.8

Q ss_pred             CCceEEeCCCCCCCCcHHHHHHHh-hhccccccccEEeecCCCCc------eeeecccc-----ccccccccc------c
Q psy15852         29 DDRKLFCPLSSYLELDYLQLWQYF-DWVSSSFSENCLLEDSIGKP------LTVSCSHH-----YYLFDQILR------T   90 (661)
Q Consensus        29 ~~r~lfVg~l~~~~te~~~l~~~F-~~g~~~~~~~~~~~d~~~~~------~~~~~~~~-----~~l~~~~~r------~   90 (661)
                      +.-|||||.||..++| ++|+++| +||  .|.+|.+++|..+..      |++...++     ..|++...-      .
T Consensus        33 ~~vKlfVgqIprt~sE-~dlr~lFe~yg--~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv  109 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASE-KDLRELFEKYG--NVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV  109 (510)
T ss_pred             hhhhheeccCCccccH-HHHHHHHHHhC--ceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence            5678999999999999 9999999 999  999999999988876      44444433     122221111      1


Q ss_pred             --eeee-eecC---CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHH
Q psy15852         91 --HFFY-IMEA---KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIA  164 (661)
Q Consensus        91 --~~~~-~~~~---~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~  164 (661)
                        .+++ +.++   .+++|++.+...+||.|++++|++||.|++|.|++|.. +.+||||||.|.+.|.|..|    +..
T Consensus       110 qvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~A----ika  184 (510)
T KOG0144|consen  110 QVKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAA----IKA  184 (510)
T ss_pred             eecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHH----HHh
Confidence              1111 2222   56788888888999999999999999999999999976 99999999999999999999    999


Q ss_pred             hCCe-eecc--eeehhhhhhccC---------------------------------------------------------
Q psy15852        165 EGNH-VINN--KKIEAKKAKAKS---------------------------------------------------------  184 (661)
Q Consensus       165 ~~~~-~i~g--~~i~v~~~~~~~---------------------------------------------------------  184 (661)
                      +|+. .+.|  .+|.|++++++.                                                         
T Consensus       185 ~ng~~tmeGcs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~  264 (510)
T KOG0144|consen  185 LNGTQTMEGCSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLP  264 (510)
T ss_pred             hccceeeccCCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCccccccc
Confidence            9875 4444  677787776543                                                         


Q ss_pred             --------------------------------------------------------------------------------
Q psy15852        185 --------------------------------------------------------------------------------  184 (661)
Q Consensus       185 --------------------------------------------------------------------------------  184 (661)
                                                                                                      
T Consensus       265 ~L~~l~a~~~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~  344 (510)
T KOG0144|consen  265 PLGPLNATQLQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPAN  344 (510)
T ss_pred             CCCCcchhHHHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchh
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------------------------
Q psy15852        185 --------------------------------------------------------------------------------  184 (661)
Q Consensus       185 --------------------------------------------------------------------------------  184 (661)
                                                                                                      
T Consensus       345 ~n~~~~~a~a~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeG  424 (510)
T KOG0144|consen  345 YNLAGGMAGAGTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEG  424 (510)
T ss_pred             cccccccccccccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCc
Confidence                                                                                            


Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      .+|||.+||.+.-+.+|-..|..||.|.+.++..|+.|+.++.|+||.|++..+|..||..+ +..++.++++|.....+
T Consensus       425 anlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~  504 (510)
T KOG0144|consen  425 ANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDR  504 (510)
T ss_pred             cceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeecc
Confidence            57999999999999999999999999999999999999999999999999999999999998 57899999999988776


Q ss_pred             CC
Q psy15852        264 PE  265 (661)
Q Consensus       264 ~~  265 (661)
                      ..
T Consensus       505 ~n  506 (510)
T KOG0144|consen  505 NN  506 (510)
T ss_pred             CC
Confidence            53

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.93  E-value=2.4e-24  Score=238.01  Aligned_cols=224  Identities=17%  Similarity=0.273  Sum_probs=173.7

Q ss_pred             CCceEEeCCCCCCCCcHHHHHHHh-hhccccccccEEeecCCCCc------eeeecccc---------ccccccccccee
Q psy15852         29 DDRKLFCPLSSYLELDYLQLWQYF-DWVSSSFSENCLLEDSIGKP------LTVSCSHH---------YYLFDQILRTHF   92 (661)
Q Consensus        29 ~~r~lfVg~l~~~~te~~~l~~~F-~~g~~~~~~~~~~~d~~~~~------~~~~~~~~---------~~l~~~~~r~~~   92 (661)
                      +.++|||+|||+.+++ ++|+++| ++|  .|.++.+++|..+..      |.|...+.         ..+.+.......
T Consensus        88 ~~~~l~V~nlp~~~~~-~~l~~~F~~~G--~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        88 DDRTVFVLQLALKARE-RDLYEFFSKVG--KVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQS  164 (457)
T ss_pred             CCcEEEEeCCCCCCCH-HHHHHHHHhcC--CeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEee
Confidence            5789999999999999 9999999 999  999999999865543      33332221         011111111100


Q ss_pred             e---------------eeecCCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHh
Q psy15852         93 F---------------YIMEAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA  157 (661)
Q Consensus        93 ~---------------~~~~~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A  157 (661)
                      .               ...+...++++.++++.+++++|+++|++||.|..|.|++++.+|+++|||||+|.+.++|.+|
T Consensus       165 ~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A  244 (457)
T TIGR01622       165 SQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA  244 (457)
T ss_pred             cchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHH
Confidence            0               0011123444444445999999999999999999999999999899999999999999999999


Q ss_pred             hHHHHHHhCCeeecceeehhhhhhc-------------------------------------------------------
Q psy15852        158 SVEDVIAEGNHVINNKKIEAKKAKA-------------------------------------------------------  182 (661)
Q Consensus       158 ~~~~~~~~~~~~i~g~~i~v~~~~~-------------------------------------------------------  182 (661)
                          +..+++..|.|++|.|.++..                                                       
T Consensus       245 ----~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  320 (457)
T TIGR01622       245 ----LEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIA  320 (457)
T ss_pred             ----HHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhh
Confidence                889999999999999987321                                                       


Q ss_pred             ----------------------------------------cCCeeEecCCCccCC----------HHHHHHHHhcCCCeE
Q psy15852        183 ----------------------------------------KSGKIFVGGLSPEMK----------DEEIKAHFAQFGNII  212 (661)
Q Consensus       183 ----------------------------------------~~~~lfV~nLp~~~t----------e~~L~~~F~~~G~i~  212 (661)
                                                              ..++|+|.||....+          .+||++.|++||.|.
T Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~  400 (457)
T TIGR01622       321 LMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVV  400 (457)
T ss_pred             hhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCee
Confidence                                                    014577888844333          368999999999999


Q ss_pred             EEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        213 ETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       213 ~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      .|.|..    ....|++||+|.++++|.+|++.+ +..++|+.|.+.+....
T Consensus       401 ~v~v~~----~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       401 HIYVDT----KNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVND  448 (457)
T ss_pred             EEEEeC----CCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHH
Confidence            999864    345799999999999999999998 68999999999988654

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.

>KOG4212|consensus

Probab=99.91  E-value=2.8e-22  Score=201.15  Aligned_cols=79  Identities=16%  Similarity=0.347  Sum_probs=71.7

Q ss_pred             CCeeEecCCCccCCHHHHHHHHh-cCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC-CccCCeEEEEEecc
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFA-QFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK-QKINDKEVDVKKAT  261 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~-~~~~g~~i~V~~a~  261 (661)
                      .+.+||.|||+++.+.+|+++|. +.|+|+.|.++.|.. |+++|+|.|+|+++|.++||++.++ +.+.||+|.|+...
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~-GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDES-GKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccC-CCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            35699999999999999999995 589999999999875 9999999999999999999999985 78999999998766


Q ss_pred             CC
Q psy15852        262 PK  263 (661)
Q Consensus       262 ~k  263 (661)
                      ..
T Consensus       123 d~  124 (608)
T KOG4212|consen  123 DE  124 (608)
T ss_pred             ch
Confidence            53

>KOG0131|consensus

Probab=99.90  E-value=1e-23  Score=189.13  Aligned_cols=162  Identities=22%  Similarity=0.343  Sum_probs=146.7

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++|++|++ .++++.|.++|-+.|+|.++++++|+.+...+|||||+|.++|+|+-|    +.-+|...+.|++|+|.
T Consensus         9 d~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYA----ikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    9 DATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYA----IKILNMVKLYGRPIRVN   84 (203)
T ss_pred             CceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHH----HHHHHHHHhcCceeEEE
Confidence            4455555555 999999999999999999999999999999999999999999999999    99999999999999998


Q ss_pred             hhhcc------CCeeEecCCCccCCHHHHHHHHhcCCCeEE-EEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCcc
Q psy15852        179 KAKAK------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIE-TEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKI  250 (661)
Q Consensus       179 ~~~~~------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~-v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~  250 (661)
                      .+...      ..+|||+||.+.++|..|.+.|+.||.+.. -++++++.||.++|||||.|.+.+.+.+|+..+ ++.+
T Consensus        85 kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l  164 (203)
T KOG0131|consen   85 KASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYL  164 (203)
T ss_pred             ecccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchh
Confidence            87632      258999999999999999999999998765 488999999999999999999999999999998 6889


Q ss_pred             CCeEEEEEeccCCCC
Q psy15852        251 NDKEVDVKKATPKPE  265 (661)
Q Consensus       251 ~g~~i~V~~a~~k~~  265 (661)
                      ..++|.|.++..+..
T Consensus       165 ~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  165 CNRPITVSYAFKKDT  179 (203)
T ss_pred             cCCceEEEEEEecCC
Confidence            999999999987653

>KOG0124|consensus

Probab=99.89  E-value=1.4e-21  Score=191.90  Aligned_cols=160  Identities=19%  Similarity=0.453  Sum_probs=146.7

Q ss_pred             EEEEcCC-CcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        102 MVSHPGI-VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       102 ~~~~~~~-~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      -+|++.+ ++..|+.|+..|..||+|++|.+..|+.|+++||||||+|+-+|.|+.|    ...+|+..+.||.|+|.+.
T Consensus       115 RvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLA----lEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  115 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLA----LEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             heeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHH----HHHhccccccCccccccCC
Confidence            3455554 5999999999999999999999999999999999999999999999999    8999999999999999865


Q ss_pred             hccC----------------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHH
Q psy15852        181 KAKS----------------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK  244 (661)
Q Consensus       181 ~~~~----------------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~  244 (661)
                      ....                ++|||..+-++++++||+.+|+.||+|..|.+.+++.++.++||+|++|.+..+...|+.
T Consensus       191 sNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAia  270 (544)
T KOG0124|consen  191 SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA  270 (544)
T ss_pred             CCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhh
Confidence            4322                789999999999999999999999999999999999989999999999999999999999


Q ss_pred             hCC-CccCCeEEEEEeccCCCC
Q psy15852        245 NPK-QKINDKEVDVKKATPKPE  265 (661)
Q Consensus       245 ~~~-~~~~g~~i~V~~a~~k~~  265 (661)
                      .++ ..++|+.|+|..+...+.
T Consensus       271 sMNlFDLGGQyLRVGk~vTPP~  292 (544)
T KOG0124|consen  271 SMNLFDLGGQYLRVGKCVTPPD  292 (544)
T ss_pred             hcchhhcccceEecccccCCCc
Confidence            997 689999999998876655

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.89  E-value=2.8e-22  Score=219.60  Aligned_cols=181  Identities=18%  Similarity=0.365  Sum_probs=147.0

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+++++++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++|++.+ +..+.|+.|+|.+.
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            44589999999999999999999999999999999999999999999999999999999999987 68899999999853


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCccc
Q psy15852        261 TPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEV  340 (661)
Q Consensus       261 ~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (661)
                      .......                                                                   +.... 
T Consensus       185 ~~~p~a~-------------------------------------------------------------------~~~~~-  196 (612)
T TIGR01645       185 SNMPQAQ-------------------------------------------------------------------PIIDM-  196 (612)
T ss_pred             ccccccc-------------------------------------------------------------------ccccc-
Confidence            3211000                                                                   00000 


Q ss_pred             CCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCC
Q psy15852        341 DVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTT  420 (661)
Q Consensus       341 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~  420 (661)
                                  ..               .+             .....++++.++.+.+++++|+++|+.|        
T Consensus       197 ------------~~---------------~~-------------~~~~~rLfVgnLp~~vteedLk~lFs~F--------  228 (612)
T TIGR01645       197 ------------VQ---------------EE-------------AKKFNRIYVASVHPDLSETDIKSVFEAF--------  228 (612)
T ss_pred             ------------cc---------------cc-------------ccccceEEeecCCCCCCHHHHHHHHhhc--------
Confidence                        00               00             0001245666666779999999999888        


Q ss_pred             cccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHH-hCCCCcCCCcEEEEecCCCCCC
Q psy15852        421 TEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL-KNPKQKINDKEVDVKKATPKPE  499 (661)
Q Consensus       421 ~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai-~~~~~~l~g~~i~v~~a~~~~~  499 (661)
                                            |+|.+++++.|..+++++|||||.|.+.++|.+|+ ..++..++|+.|.|.++.+.+.
T Consensus       229 ----------------------G~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP~  286 (612)
T TIGR01645       229 ----------------------GEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPD  286 (612)
T ss_pred             ----------------------CCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCcc
Confidence                                  78999999999999999999999999999999999 5556889999999999987654


Q ss_pred             C
Q psy15852        500 P  500 (661)
Q Consensus       500 ~  500 (661)
                      .
T Consensus       287 ~  287 (612)
T TIGR01645       287 A  287 (612)
T ss_pred             c
Confidence            3

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.

>KOG0110|consensus

Probab=99.88  E-value=2.3e-22  Score=214.32  Aligned_cols=250  Identities=18%  Similarity=0.291  Sum_probs=193.1

Q ss_pred             CCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852         98 AKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus        98 ~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ..+++++++|+| .+..++|.++|..||+|..|.++..   |.   -++|+|.++.+|.+|    ...+....+...++.
T Consensus       383 rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~---G~---~aiv~fl~p~eAr~A----frklaysr~k~~ply  452 (725)
T KOG0110|consen  383 RSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPG---GT---GAIVEFLNPLEARKA----FRKLAYSRFKSAPLY  452 (725)
T ss_pred             hhcceeeeccCccccccHHHHHHhhcccccceeecCcc---cc---eeeeeecCccchHHH----HHHhchhhhccCccc
Confidence            345788888888 9999999999999999999966632   22   389999999999999    666666666655555


Q ss_pred             hhhhhcc-------------------------------------------------------CCeeEecCCCccCCHHHH
Q psy15852        177 AKKAKAK-------------------------------------------------------SGKIFVGGLSPEMKDEEI  201 (661)
Q Consensus       177 v~~~~~~-------------------------------------------------------~~~lfV~nLp~~~te~~L  201 (661)
                      +.|+...                                                       .++|||+||+++++.++|
T Consensus       453 le~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l  532 (725)
T KOG0110|consen  453 LEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDL  532 (725)
T ss_pred             cccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHH
Confidence            4443100                                                       034999999999999999


Q ss_pred             HHHHhcCCCeEEEEeccCCCC---CCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCCCCCCCCCCCCCCC
Q psy15852        202 KAHFAQFGNIIETEMPYDKSK---SQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKPEPFGVRGGRGGRG  277 (661)
Q Consensus       202 ~~~F~~~G~i~~v~i~~~~~~---g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~~~~~~~~~~~~~g  277 (661)
                      ..+|.+.|.|.++.|...++.   -.+.|||||+|.+.++|+.|++.| ++.++|+.|.|+++..++....         
T Consensus       533 ~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~---------  603 (725)
T KOG0110|consen  533 EDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTV---------  603 (725)
T ss_pred             HHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCcccccc---------
Confidence            999999999999988876542   135599999999999999999998 5899999999999884332100         


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCCCccEEEEecCCCCCC
Q psy15852        278 GRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKNHNS  357 (661)
Q Consensus       278 ~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  357 (661)
                                                                                               | +..  
T Consensus       604 -------------------------------------------------------------------------g-K~~--  607 (725)
T KOG0110|consen  604 -------------------------------------------------------------------------G-KKK--  607 (725)
T ss_pred             -------------------------------------------------------------------------c-ccc--
Confidence                                                                                     0 000  


Q ss_pred             CCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCC-cCccchhhhhhccCcccccCCcccchhhcccccccch
Q psy15852        358 DENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPS-IRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHME  436 (661)
Q Consensus       358 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~-~~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~  436 (661)
                               +.+                .-... |+..++|. .+-.+++.+|..|                        
T Consensus       608 ---------~~k----------------k~~tK-IlVRNipFeAt~rEVr~LF~aF------------------------  637 (725)
T KOG0110|consen  608 ---------SKK----------------KKGTK-ILVRNIPFEATKREVRKLFTAF------------------------  637 (725)
T ss_pred             ---------ccc----------------cccce-eeeeccchHHHHHHHHHHHhcc------------------------
Confidence                     000                00112 34445566 8888899999888                        


Q ss_pred             hhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHhC-CCCcCCCcEEEEecCCCCC
Q psy15852        437 VTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN-PKQKINDKEVDVKKATPKP  498 (661)
Q Consensus       437 ~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~~-~~~~l~g~~i~v~~a~~~~  498 (661)
                            |.+..|+||.....+.++|||||.|-++.+|..|+.. ....|-|++|.+.||....
T Consensus       638 ------GqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  638 ------GQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             ------cceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence                  8899999999877778899999999999999999944 3577999999999988653

>KOG4205|consensus

Probab=99.86  E-value=1.6e-21  Score=197.10  Aligned_cols=167  Identities=34%  Similarity=0.613  Sum_probs=155.6

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ...++|+.++.++++++.|++.|++||+|.+|.+++|+.++++|||+||+|++++...+     ++....+.|.|+.|.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~-----vl~~~~h~~dgr~ve~   79 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDA-----VLNARTHKLDGRSVEP   79 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchhe-----eecccccccCCccccc
Confidence            45789999999999999999999999999999999999999999999999999999999     6777889999999999


Q ss_pred             hhhhccC-----------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC
Q psy15852        178 KKAKAKS-----------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP  246 (661)
Q Consensus       178 ~~~~~~~-----------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~  246 (661)
                      +.+.++.           ++|||++||.++++++|+++|.+||.|..+.++.|..+++++||+||.|.+++++.+++...
T Consensus        80 k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~  159 (311)
T KOG4205|consen   80 KRAVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQK  159 (311)
T ss_pred             eeccCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccc
Confidence            8886653           48999999999999999999999999999999999999999999999999999999999888


Q ss_pred             CCccCCeEEEEEeccCCCCCCCC
Q psy15852        247 KQKINDKEVDVKKATPKPEPFGV  269 (661)
Q Consensus       247 ~~~~~g~~i~V~~a~~k~~~~~~  269 (661)
                      -+.|+++.+.|+.|.++......
T Consensus       160 f~~~~gk~vevkrA~pk~~~~~~  182 (311)
T KOG4205|consen  160 FHDFNGKKVEVKRAIPKEVMQST  182 (311)
T ss_pred             eeeecCceeeEeeccchhhcccc
Confidence            89999999999999999876543

>KOG4211|consensus

Probab=99.85  E-value=4.6e-20  Score=189.43  Aligned_cols=313  Identities=21%  Similarity=0.269  Sum_probs=192.6

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKP  264 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k~  264 (661)
                      .-|.+++||+++|++||.++|+.++ |+++.+.+.  +|+..|-|||+|.+.+++++|+++....+..|-|+|-.+...+
T Consensus        11 ~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~e   87 (510)
T KOG4211|consen   11 FEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR--NGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGAE   87 (510)
T ss_pred             eEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc--CCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCcc
Confidence            4578899999999999999999986 888777654  5899999999999999999999998888999999999887665


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCCCc
Q psy15852        265 EPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTG  344 (661)
Q Consensus       265 ~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (661)
                      ...-.+..                                                       .|...            
T Consensus        88 ~d~~~~~~-------------------------------------------------------g~~s~------------  100 (510)
T KOG4211|consen   88 ADWVMRPG-------------------------------------------------------GPNSS------------  100 (510)
T ss_pred             ccccccCC-------------------------------------------------------CCCCC------------
Confidence            32111000                                                       00000            


Q ss_pred             cEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCC-cCccchhhhhhccCcccccCCccc
Q psy15852        345 VIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPS-IRELEIPEAFLTKTTTVPMTTTEH  423 (661)
Q Consensus       345 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~-~~~~~l~~~f~~~~~~~~~~~~~~  423 (661)
                                                                ..+-++--..+|. +++++|.++|+...          
T Consensus       101 ------------------------------------------~~d~vVRLRGLPfscte~dI~~FFaGL~----------  128 (510)
T KOG4211|consen  101 ------------------------------------------ANDGVVRLRGLPFSCTEEDIVEFFAGLE----------  128 (510)
T ss_pred             ------------------------------------------CCCceEEecCCCccCcHHHHHHHhcCCc----------
Confidence                                                      0011222234566 89999999998763          


Q ss_pred             chhhcccccccchhhccCCceeEE--eeecccccCCcccceEEEEeCChHHHHHHHhCCCCcCCCcEEEEecCCCCCCCC
Q psy15852        424 MVLVTGTDMMHMEVTEAVPMEIIE--TEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEPF  501 (661)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~G~i~~--~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~~~~~~l~g~~i~v~~a~~~~~~~  501 (661)
                                           |..  +-+++|.. +++.|-|||+|.+++.|++|+..+...|..+.|+|-++.......
T Consensus       129 ---------------------Iv~~gi~l~~d~r-gR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~Ss~~e~~~  186 (510)
T KOG4211|consen  129 ---------------------IVPDGILLPMDQR-GRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRSSRAEVKR  186 (510)
T ss_pred             ---------------------ccccceeeeccCC-CCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehhHHHHHHh
Confidence                                 333  33555544 558899999999999999999999999999999998875443221


Q ss_pred             CC--CCCCCCC-CCCC----CCCCCC-CCCCC------CCCCCCCCCCCCCCccccccccccCCCccccccccccCCCCC
Q psy15852        502 GV--RGGRGGR-GGRG----GRGGRM-AGGYG------GYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPL  567 (661)
Q Consensus       502 ~~--~~~~~~~-~~~~----~~~~~~-~~g~g------g~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~  567 (661)
                      ..  ..+..++ +.+-    ++++.. ..+.+      -++.++.++  +++...+...+.......   ..+.....|.
T Consensus       187 ~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~--~g~~~~~~~~d~~~~gs~---~~~~~~~~~~  261 (510)
T KOG4211|consen  187 AAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGY--YGFSRYPSLQDYGNFGSY---GGGRDPNYPV  261 (510)
T ss_pred             hccccccccCCCCccccccCCccccccccccCCCccccccccccCCc--cccccCcccccccccccc---ccccccccCC
Confidence            11  0000110 0000    011000 00000      000000010  001111111110000000   0000000110


Q ss_pred             cccCCCccccccCCCCccccccccCCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHH
Q psy15852        568 TVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES  647 (661)
Q Consensus       568 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~  647 (661)
                      .   +..+..   ...............+..++||++.++.+|.++|++.-.+ .|+|-..++ |+..|.|+|+|.|.++
T Consensus       262 ~---~g~~~~---g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~d-Gr~TGEAdveF~t~ed  333 (510)
T KOG4211|consen  262 S---SGPHRQ---GGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGPD-GRATGEADVEFATGED  333 (510)
T ss_pred             C---CCcccC---CCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCCC-CccCCcceeecccchh
Confidence            0   000000   1111111112233678999999999999999999999666 999998876 9999999999999999


Q ss_pred             HHHHHHh
Q psy15852        648 LEKASVE  654 (661)
Q Consensus       648 A~~A~~~  654 (661)
                      |..||.+
T Consensus       334 av~Amsk  340 (510)
T KOG4211|consen  334 AVGAMGK  340 (510)
T ss_pred             hHhhhcc
Confidence            9999986

>KOG0147|consensus

Probab=99.83  E-value=6.7e-20  Score=190.75  Aligned_cols=157  Identities=23%  Similarity=0.400  Sum_probs=140.2

Q ss_pred             EEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhhc
Q psy15852        104 SHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKA  182 (661)
Q Consensus       104 ~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~~  182 (661)
                      +...+. ..+..+|.++|+.+|+|.+|+++.|+.+++++|.|||+|.+.++...|     ..|.|+.+.|.+|.|+....
T Consensus       183 f~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~a-----iaLsGqrllg~pv~vq~sEa  257 (549)
T KOG0147|consen  183 FCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLA-----IALSGQRLLGVPVIVQLSEA  257 (549)
T ss_pred             HHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhH-----hhhcCCcccCceeEecccHH
Confidence            333343 788999999999999999999999999999999999999999999995     68999999999999876532


Q ss_pred             cC-------------------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHH
Q psy15852        183 KS-------------------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL  243 (661)
Q Consensus       183 ~~-------------------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al  243 (661)
                      ..                   .+|||+||-+++++++|+.+|++||.|+.|.+++|..||.++||+||+|.+.++|.+|+
T Consensus       258 eknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~  337 (549)
T KOG0147|consen  258 EKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKAL  337 (549)
T ss_pred             HHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHH
Confidence            21                   34999999999999999999999999999999999999999999999999999999998


Q ss_pred             HhC-CCccCCeEEEEEeccCCCC
Q psy15852        244 KNP-KQKINDKEVDVKKATPKPE  265 (661)
Q Consensus       244 ~~~-~~~~~g~~i~V~~a~~k~~  265 (661)
                      ..+ +..|-|+.|+|.....+..
T Consensus       338 e~lngfelAGr~ikV~~v~~r~~  360 (549)
T KOG0147|consen  338 EQLNGFELAGRLIKVSVVTERVD  360 (549)
T ss_pred             HHhccceecCceEEEEEeeeecc
Confidence            887 6899999999987766543

>KOG0109|consensus

Probab=99.82  E-value=2.9e-20  Score=178.32  Aligned_cols=150  Identities=21%  Similarity=0.432  Sum_probs=136.5

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      ++||++|+..+++.+|+.+|++||+|++|.|+++        ||||..++...|+.|    |..|++..|+|..|.|+.+
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaeda----irNLhgYtLhg~nInVeaS   71 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDA----IRNLHGYTLHGVNINVEAS   71 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHH----HhhcccceecceEEEEEec
Confidence            5666666669999999999999999999999986        999999999999999    9999999999999999998


Q ss_pred             hccC---CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEE
Q psy15852        181 KAKS---GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVD  256 (661)
Q Consensus       181 ~~~~---~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~  256 (661)
                      +.++   .+|+|+||.+.++..+|+..|++||+|.+|+|+        ++|+||.|+..++|..|++.+ +..++|++++
T Consensus        72 ksKsk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv--------kdy~fvh~d~~eda~~air~l~~~~~~gk~m~  143 (346)
T KOG0109|consen   72 KSKSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV--------KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMH  143 (346)
T ss_pred             cccCCCccccccCCCCccccCHHHhhhhcccCCceeeeee--------cceeEEEEeeccchHHHHhcccccccccceee
Confidence            8773   689999999999999999999999999999997        679999999999999999998 6899999999


Q ss_pred             EEeccCCCCCCCCC
Q psy15852        257 VKKATPKPEPFGVR  270 (661)
Q Consensus       257 V~~a~~k~~~~~~~  270 (661)
                      |....++-....+.
T Consensus       144 vq~stsrlrtapgm  157 (346)
T KOG0109|consen  144 VQLSTSRLRTAPGM  157 (346)
T ss_pred             eeeeccccccCCCC
Confidence            99998876554333

>KOG0146|consensus

Probab=99.82  E-value=1.5e-19  Score=171.04  Aligned_cols=94  Identities=24%  Similarity=0.393  Sum_probs=81.3

Q ss_pred             ceeehhhhhhcc-----CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC
Q psy15852        172 NKKIEAKKAKAK-----SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP  246 (661)
Q Consensus       172 g~~i~v~~~~~~-----~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~  246 (661)
                      +|+|.|+++..+     +++|||+-|.+.-.|+|++.+|..||.|++|.+.+..+ |.+||+|||+|.+..+|+.||..+
T Consensus         2 nrpiqvkpadsesrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqaAI~aL   80 (371)
T KOG0146|consen    2 NRPIQVKPADSESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQAAINAL   80 (371)
T ss_pred             CCCccccccccccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccchHHHHHHHHh
Confidence            467888887654     47899999999999999999999999999999999877 899999999999999999999997


Q ss_pred             -C-CccCC--eEEEEEeccCCCCC
Q psy15852        247 -K-QKIND--KEVDVKKATPKPEP  266 (661)
Q Consensus       247 -~-~~~~g--~~i~V~~a~~k~~~  266 (661)
                       + .++-|  ..|.|+++....++
T Consensus        81 HgSqTmpGASSSLVVK~ADTdkER  104 (371)
T KOG0146|consen   81 HGSQTMPGASSSLVVKFADTDKER  104 (371)
T ss_pred             cccccCCCCccceEEEeccchHHH
Confidence             2 56666  56889988776553

>KOG1190|consensus

Probab=99.82  E-value=4.1e-18  Score=170.53  Aligned_cols=396  Identities=15%  Similarity=0.136  Sum_probs=236.5

Q ss_pred             CCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         99 KNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        99 ~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ..+++...|+| +++|+||.+++..||.|+.+.+.+.++      -||++|.++++|..- .. ....-...+.+++|.+
T Consensus        27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn------QAflem~d~~sAvtm-v~-~y~~~~p~lr~~~~yi   98 (492)
T KOG1190|consen   27 PSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN------QAFLEMADEESAVTM-VN-YYTSVTPVLRGQPIYI   98 (492)
T ss_pred             CcceeEeccCCccccHHHHHHhcccccceeeeeeeccch------hhhhhhcchhhhhhe-ee-cccccCccccCcceee
Confidence            45677777777 999999999999999999999988554      799999999999872 00 0111122344555554


Q ss_pred             hhhhcc---------------------------------------------CCeeEecCCCccCCHHHHHHHHhcCCCeE
Q psy15852        178 KKAKAK---------------------------------------------SGKIFVGGLSPEMKDEEIKAHFAQFGNII  212 (661)
Q Consensus       178 ~~~~~~---------------------------------------------~~~lfV~nLp~~~te~~L~~~F~~~G~i~  212 (661)
                      +++...                                             --+++|.|+-+.++-+-|..+|++||.|.
T Consensus        99 q~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~Vl  178 (492)
T KOG1190|consen   99 QYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVL  178 (492)
T ss_pred             hhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeE
Confidence            442110                                             02578899999999999999999999998


Q ss_pred             EEEeccCCCCCCcCcE-EEEEeCCHHHHHHHHHhC-CCccC-C-eEEEEEeccCCCCCC--CCCCCCCCCCCCCCCCCCC
Q psy15852        213 ETEMPYDKSKSQRKNF-CFITFEHESVVIDLLKNP-KQKIN-D-KEVDVKKATPKPEPF--GVRGGRGGRGGRGGRGGRM  286 (661)
Q Consensus       213 ~v~i~~~~~~g~~~g~-afV~f~~~~~A~~Al~~~-~~~~~-g-~~i~V~~a~~k~~~~--~~~~~~~~~g~~~g~~~~~  286 (661)
                      .|.-..     ++.+| |.|+|.+.+.|+.|-..+ +..|. | ..|+|.+++-..-.-  .....|..-.         
T Consensus       179 KIiTF~-----Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTn---------  244 (492)
T KOG1190|consen  179 KIITFT-----KNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTN---------  244 (492)
T ss_pred             EEEEEe-----cccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccC---------
Confidence            876553     23455 899999999999998776 44332 3 556665543211100  0000000000         


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCC
Q psy15852        287 AGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSH  366 (661)
Q Consensus       287 ~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~  366 (661)
                           .+-+.|  -+..+.++.+-     ....       ..|..+. .|.      ..+   .+....    +.+.   
T Consensus       245 -----p~LP~g--d~~p~l~~~~~-----aa~~-------~~~~~~g-~p~------aip---~~~~~a----~~a~---  288 (492)
T KOG1190|consen  245 -----PDLPVG--DGQPSLDQLMA-----AAFG-------SVPAVHG-APL------AIP---SGAAGA----NAAD---  288 (492)
T ss_pred             -----CCCCCC--ccccccchhhh-----cccc-------ccccccC-Ccc------cCC---ccchhh----cccc---
Confidence                 000000  00000000000     0000       0000000 000      000   000000    0000   


Q ss_pred             CChhHHHhhhccccccccccccccccccCCCCC-cCccchhhhhhccCcccccCCcccchhhcccccccchhhccCCcee
Q psy15852        367 PSQNAIKLYLTRSSYREWGHVADNLLLCDNFPS-IRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEI  445 (661)
Q Consensus       367 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~-~~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i  445 (661)
                            .. .+     .-+ ...++++.++.+. +|++.|..+|..|                              |+|
T Consensus       289 ------~~-~~-----~~~-~n~vllvsnln~~~VT~d~LftlFgvY------------------------------GdV  325 (492)
T KOG1190|consen  289 ------GK-IE-----SPS-ANVVLLVSNLNEEAVTPDVLFTLFGVY------------------------------GDV  325 (492)
T ss_pred             ------cc-cc-----cCC-CceEEEEecCchhccchhHHHHHHhhh------------------------------cce
Confidence                  00 00     000 1346777788887 9999999999888                              889


Q ss_pred             EEeeecccccCCcccceEEEEeCChHHHHHHH-hCCCCcCCCcEEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy15852        446 IETEMPYDKSKSQRKNFCFITFEHESVVIDLL-KNPKQKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGY  524 (661)
Q Consensus       446 ~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai-~~~~~~l~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~  524 (661)
                      .+|+|.+++.     .-|.|++.+...|+-|+ .+.++.+.|+.|+|..++-.....+..+.. .               
T Consensus       326 qRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~egq~-d---------------  384 (492)
T KOG1190|consen  326 QRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREGQE-D---------------  384 (492)
T ss_pred             EEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccCCCCCCc-c---------------
Confidence            9999988533     67999999999999999 566799999999998766433221100000 0               


Q ss_pred             CCCCCCCCCCCCCCCccccccccccCCCccccccccccCCCCCcccCCCccccccCCCCccccccccCCCeEEEcCCCCC
Q psy15852        525 GGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVD  604 (661)
Q Consensus       525 gg~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~  604 (661)
                                  .++     ..++..              .|.        ..+..+..+.+.....+..+|...|+|.+
T Consensus       385 ------------~gl-----T~dy~~--------------spL--------hrfkkpgsKN~~ni~PpsatlHlsnip~s  425 (492)
T KOG1190|consen  385 ------------QGL-----TKDYGN--------------SPL--------HRFKKPGSKNYQNIFPPSATLHLSNIPPS  425 (492)
T ss_pred             ------------ccc-----cccCCC--------------Cch--------hhccCcccccccccCCchhheeeccCCcc
Confidence                        000     000000              011        01222223333334455678999999999


Q ss_pred             CCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCccc
Q psy15852        605 KITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY  659 (661)
Q Consensus       605 ~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~~  659 (661)
                      ++|+||+.+|..-|-..+....-.    +.+=+|.+++.++|+|..|+-.+|-+|
T Consensus       426 vsee~lk~~f~~~g~~vkafkff~----kd~kmal~q~~sveeA~~ali~~hnh~  476 (492)
T KOG1190|consen  426 VSEEDLKNLFQEPGGQVKAFKFFQ----KDRKMALPQLESVEEAIQALIDLHNHY  476 (492)
T ss_pred             cchhHHHHhhhcCCceEEeeeecC----CCcceeecccCChhHhhhhcccccccc
Confidence            999999999999988867666542    234499999999999999999886555

>KOG4205|consensus

Probab=99.81  E-value=1.5e-19  Score=182.97  Aligned_cols=178  Identities=28%  Similarity=0.460  Sum_probs=153.8

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      ..++|||++|+++++++.|+++|.+||+|.+|.+++|+.+++++||+||+|++++...++|....++|+|+.|.++.|.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            46899999999999999999999999999999999999999999999999999999999998889999999999999998


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCC
Q psy15852        263 KPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDV  342 (661)
Q Consensus       263 k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  342 (661)
                      +.++....                                                                   .+   
T Consensus        85 r~~~~~~~-------------------------------------------------------------------~~---   94 (311)
T KOG4205|consen   85 REDQTKVG-------------------------------------------------------------------RH---   94 (311)
T ss_pred             cccccccc-------------------------------------------------------------------cc---
Confidence            77542110                                                                   00   


Q ss_pred             CccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCCcc
Q psy15852        343 TGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTE  422 (661)
Q Consensus       343 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~  422 (661)
                      ..+..+++|+++                                           +.+++++++++|.++          
T Consensus        95 ~~tkkiFvGG~~-------------------------------------------~~~~e~~~r~yfe~~----------  121 (311)
T KOG4205|consen   95 LRTKKIFVGGLP-------------------------------------------PDTTEEDFKDYFEQF----------  121 (311)
T ss_pred             cceeEEEecCcC-------------------------------------------CCCchHHHhhhhhcc----------
Confidence            022335555443                                           457788888888777          


Q ss_pred             cchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHhCCCCcCCCcEEEEecCCCCCCCCC
Q psy15852        423 HMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEPFG  502 (661)
Q Consensus       423 ~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~~~~~~l~g~~i~v~~a~~~~~~~~  502 (661)
                                          |.|..+.+++|..+.+++||+||.|++++++.+++.+..+.|+++.++|++|.++..+..
T Consensus       122 --------------------g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f~~~~gk~vevkrA~pk~~~~~  181 (311)
T KOG4205|consen  122 --------------------GKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKFHDFNGKKVEVKRAIPKEVMQS  181 (311)
T ss_pred             --------------------ceeEeeEEeecccccccccceeeEeccccccceecccceeeecCceeeEeeccchhhccc
Confidence                                779999999999999999999999999999999999999999999999999999987764


Q ss_pred             C
Q psy15852        503 V  503 (661)
Q Consensus       503 ~  503 (661)
                      .
T Consensus       182 ~  182 (311)
T KOG4205|consen  182 T  182 (311)
T ss_pred             c
Confidence            4

>KOG1456|consensus

Probab=99.80  E-value=1.8e-16  Score=156.92  Aligned_cols=398  Identities=13%  Similarity=0.076  Sum_probs=238.5

Q ss_pred             cEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        101 KMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       101 ~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      -++.+.++. .++|.+|.+.++.||+|.-|..+..+.      -|.|+|++.+.|+.++ + ....+...+.|+.-.+.+
T Consensus        32 pvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r------~alvefedi~~akn~V-n-faa~n~i~i~gq~Al~Ny  103 (494)
T KOG1456|consen   32 PVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKR------QALVEFEDIEGAKNCV-N-FAADNQIYIAGQQALFNY  103 (494)
T ss_pred             ceEEEeccccccchhHHHHHHhcCCceEEEEeccccc------eeeeeeccccchhhhe-e-hhccCcccccCchhhccc
Confidence            455555555 999999999999999998888876543      7999999999999961 1 123455556666555544


Q ss_pred             hhcc--------C---Ce---eEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHh
Q psy15852        180 AKAK--------S---GK---IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN  245 (661)
Q Consensus       180 ~~~~--------~---~~---lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~  245 (661)
                      +..+        +   ++   +-|-|--+.+|-+-|..++...|+|..|.|++..     ---|.|+|++.+.|++|-+.
T Consensus       104 Stsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkn-----gVQAmVEFdsv~~AqrAk~a  178 (494)
T KOG1456|consen  104 STSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKN-----GVQAMVEFDSVEVAQRAKAA  178 (494)
T ss_pred             chhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEecc-----ceeeEEeechhHHHHHHHhh
Confidence            4211        1   22   2344656679999999999999999999998642     23499999999999999998


Q ss_pred             CC---CccCCeEEEEEeccCCCCCCC--CCCCCC------------CCC--CCCCCCCCCCCCCCCCC----CCCCC-CC
Q psy15852        246 PK---QKINDKEVDVKKATPKPEPFG--VRGGRG------------GRG--GRGGRGGRMAGGYGGYG----GYGGG-YG  301 (661)
Q Consensus       246 ~~---~~~~g~~i~V~~a~~k~~~~~--~~~~~~------------~~g--~~~g~~~~~~~~~g~~~----g~~~~-~~  301 (661)
                      ++   .+-+-..|+|++|++..-.-.  ....+.            +++  -|.+...-.+..+..++    +|++| ++
T Consensus       179 lNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~  258 (494)
T KOG1456|consen  179 LNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRH  258 (494)
T ss_pred             cccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccC
Confidence            84   344558899999987543100  000010            111  01111111111111122    22222 33


Q ss_pred             CCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccc
Q psy15852        302 GILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSY  381 (661)
Q Consensus       302 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  381 (661)
                      +.++.++..|....+..+        ++.    +|  .....+..++.-| +                            
T Consensus       259 ~p~~~~P~r~~~~~~~~~--------g~a----~p--~g~~~g~VmMVyG-L----------------------------  295 (494)
T KOG1456|consen  259 GPPHPPPSRYRDGYRDGR--------GYA----SP--GGGAPGCVMMVYG-L----------------------------  295 (494)
T ss_pred             CCCCCCCCCCccccccCC--------CCC----CC--CCCCCCcEEEEEe-c----------------------------
Confidence            334444444422221111        000    00  1111122222222 2                            


Q ss_pred             cccccccccccccCCCCC-cCccchhhhhhccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCccc
Q psy15852        382 REWGHVADNLLLCDNFPS-IRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRK  460 (661)
Q Consensus       382 ~~~g~~~~~~~~~~~~p~-~~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~  460 (661)
                                     .-. +..+.|..+|=.|                              |+|+.|+..+.     ..
T Consensus       296 ---------------dh~k~N~drlFNl~ClY------------------------------GNV~rvkFmkT-----k~  325 (494)
T KOG1456|consen  296 ---------------DHGKMNCDRLFNLFCLY------------------------------GNVERVKFMKT-----KP  325 (494)
T ss_pred             ---------------cccccchhhhhhhhhhc------------------------------CceeeEEEeec-----cc
Confidence                           222 4555666666666                              78999997763     33


Q ss_pred             ceEEEEeCChHHHHHHH-hCCCCcCCCcEEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy15852        461 NFCFITFEHESVVIDLL-KNPKQKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELDY  539 (661)
Q Consensus       461 g~aFV~F~~~e~A~~Ai-~~~~~~l~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~~~~~~~  539 (661)
                      |.|.|+..+..+.++|+ .+++..+-|.+|.|..++..-......-..                               -
T Consensus       326 gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~~pflL-------------------------------p  374 (494)
T KOG1456|consen  326 GTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPVQPFLL-------------------------------P  374 (494)
T ss_pred             ceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccccccCCceec-------------------------------C
Confidence            89999999999999999 566677889999887766443221100000                               0


Q ss_pred             ccccccccccCCCccccccccccCCCCCcccCCCccccccCCCCccccccccCCCeEEEcCCCCCCCHHHHHHHhhcCCC
Q psy15852        540 LQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGE  619 (661)
Q Consensus       540 ~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~te~dL~~~F~~~G~  619 (661)
                      .+.+.+.+++.|...                      .+..+..........+.+.|...|.|..+||+.|.++|..-+.
T Consensus       375 DgSpSfKdys~SkNn----------------------RFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v  432 (494)
T KOG1456|consen  375 DGSPSFKDYSGSKNN----------------------RFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDV  432 (494)
T ss_pred             CCCcchhhccccccc----------------------ccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCC
Confidence            011112222222111                      0000000011111234678999999999999999999987764


Q ss_pred             e-eEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCccc
Q psy15852        620 I-ENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY  659 (661)
Q Consensus       620 I-~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~~  659 (661)
                      . ++|+|..-+. -||. -|.++|++.++|..|+...+|+=
T Consensus       433 ~~~svkvFp~ks-erSs-sGllEfe~~s~Aveal~~~NH~p  471 (494)
T KOG1456|consen  433 PPTSVKVFPLKS-ERSS-SGLLEFENKSDAVEALMKLNHYP  471 (494)
T ss_pred             CcceEEeecccc-cccc-cceeeeehHHHHHHHHHHhcccc
Confidence            3 7888887663 4444 68999999999999999988863

>KOG4212|consensus

Probab=99.78  E-value=3.6e-17  Score=164.70  Aligned_cols=155  Identities=25%  Similarity=0.428  Sum_probs=131.2

Q ss_pred             CCcEEEEcCCC-cCCHHHHHHHh-hcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852         99 KNKMVSHPGIV-HKITEELKEHF-SKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus        99 ~~~~~~~~~~~-~~te~~L~~~F-~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ..+.+|+.|+| ++.+.+|+++| ++.|+|+-|.|..|.. |++||||.|+|+++|.+++|    +..+|.+.+.|++|.
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~-GK~rGcavVEFk~~E~~qKa----~E~lnk~~~~GR~l~  117 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDES-GKARGCAVVEFKDPENVQKA----LEKLNKYEVNGRELV  117 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccC-CCcCCceEEEeeCHHHHHHH----HHHhhhccccCceEE
Confidence            34545666665 99999999999 5789999999999865 99999999999999999999    999999999999998


Q ss_pred             hhhhhccC------------------------------------------------------------------------
Q psy15852        177 AKKAKAKS------------------------------------------------------------------------  184 (661)
Q Consensus       177 v~~~~~~~------------------------------------------------------------------------  184 (661)
                      |+......                                                                        
T Consensus       118 vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lf  197 (608)
T KOG4212|consen  118 VKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLF  197 (608)
T ss_pred             EeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcc
Confidence            86543211                                                                        


Q ss_pred             ------------------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC
Q psy15852        185 ------------------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP  246 (661)
Q Consensus       185 ------------------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~  246 (661)
                                        .++||.||.+.+....|++.|.--|.|+.|.+-.|+. |.++||+.++|..+-.|..||..+
T Consensus       198 gl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKe-G~s~G~~vi~y~hpveavqaIsml  276 (608)
T KOG4212|consen  198 GLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAISML  276 (608)
T ss_pred             cchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccc-cccCCeeEEEecchHHHHHHHHhh
Confidence                              5799999999999999999999999999999999887 799999999999999999999887


Q ss_pred             C-CccCCeEEEEEe
Q psy15852        247 K-QKINDKEVDVKK  259 (661)
Q Consensus       247 ~-~~~~g~~i~V~~  259 (661)
                      + .-+..++..++.
T Consensus       277 ~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  277 DRQGLFDRRMTVRL  290 (608)
T ss_pred             ccCCCccccceeec
Confidence            4 344445544443

>KOG0146|consensus

Probab=99.78  E-value=4.7e-19  Score=167.70  Aligned_cols=164  Identities=23%  Similarity=0.384  Sum_probs=141.8

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCee-ecc--ee
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV-INN--KK  174 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~-i~g--~~  174 (661)
                      ..+++|++.+...-.|+|++.+|..||+|.+|.+.+..+ |.+||||||+|.+.-+|..|    |..+++.. +-|  ..
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqaA----I~aLHgSqTmpGASSS   92 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQAA----INALHGSQTMPGASSS   92 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccchHHHHH----HHHhcccccCCCCccc
Confidence            346777777777999999999999999999999999876 99999999999999999999    88887753 222  23


Q ss_pred             ehhhhhhccC----------------------------------------------------------------------
Q psy15852        175 IEAKKAKAKS----------------------------------------------------------------------  184 (661)
Q Consensus       175 i~v~~~~~~~----------------------------------------------------------------------  184 (661)
                      +.|++++...                                                                      
T Consensus        93 LVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~an  172 (371)
T KOG0146|consen   93 LVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNAN  172 (371)
T ss_pred             eEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhc
Confidence            3333332211                                                                      


Q ss_pred             --------------------------------------------------------------------------------
Q psy15852        185 --------------------------------------------------------------------------------  184 (661)
Q Consensus       185 --------------------------------------------------------------------------------  184 (661)
                                                                                                      
T Consensus       173 gl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~  252 (371)
T KOG0146|consen  173 GLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQ  252 (371)
T ss_pred             ccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHH
Confidence                                                                                            


Q ss_pred             ---------------------------------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEE
Q psy15852        185 ---------------------------------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFI  231 (661)
Q Consensus       185 ---------------------------------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV  231 (661)
                                                       |+|||-.||.+..+.+|-+.|-+||.|.+.++..|+.|..+|.|+||
T Consensus       253 Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFV  332 (371)
T KOG0146|consen  253 YAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFV  332 (371)
T ss_pred             HhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeE
Confidence                                             89999999999999999999999999999999999999999999999


Q ss_pred             EeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCCCC
Q psy15852        232 TFEHESVVIDLLKNP-KQKINDKEVDVKKATPKPEP  266 (661)
Q Consensus       232 ~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~~~  266 (661)
                      .|+++.+|+.||..+ +..|+-++|+|....+|...
T Consensus       333 SfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkdan  368 (371)
T KOG0146|consen  333 SFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDAN  368 (371)
T ss_pred             ecCCchhHHHHHHHhcchhhhhhhhhhhhcCccccC
Confidence            999999999999998 57899999999998887753

>KOG0147|consensus

Probab=99.77  E-value=2.4e-18  Score=179.23  Aligned_cols=179  Identities=17%  Similarity=0.206  Sum_probs=142.5

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKP  264 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k~  264 (661)
                      +++|+--|+...+.-+|.++|+.+|+|.+|.++.|+.++.++|.|||+|.+.++...||...|+-+.|.+|.|.......
T Consensus       180 Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sEaek  259 (549)
T KOG0147|consen  180 RTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSEAEK  259 (549)
T ss_pred             HHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecccHHHH
Confidence            68888888988999999999999999999999999999999999999999999999999888999999999998755432


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCCCc
Q psy15852        265 EPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTG  344 (661)
Q Consensus       265 ~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (661)
                      ......                                                         .+.       .      
T Consensus       260 nr~a~~---------------------------------------------------------s~a-------~------  269 (549)
T KOG0147|consen  260 NRAANA---------------------------------------------------------SPA-------L------  269 (549)
T ss_pred             HHHHhc---------------------------------------------------------ccc-------c------
Confidence            110000                                                         000       0      


Q ss_pred             cEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCCcccc
Q psy15852        345 VIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTEHM  424 (661)
Q Consensus       345 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~~~  424 (661)
                                                +.+.+.        |... .+++.++...++++.++.+|++|            
T Consensus       270 --------------------------~~k~~~--------~p~~-rl~vgnLHfNite~~lr~ifepf------------  302 (549)
T KOG0147|consen  270 --------------------------QGKGFT--------GPMR-RLYVGNLHFNITEDMLRGIFEPF------------  302 (549)
T ss_pred             --------------------------cccccc--------cchh-hhhhcccccCchHHHHhhhccCc------------
Confidence                                      000000        0000 14556666779999999999999            


Q ss_pred             hhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHH-hCCCCcCCCcEEEEecCCCCC
Q psy15852        425 VLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL-KNPKQKINDKEVDVKKATPKP  498 (661)
Q Consensus       425 ~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai-~~~~~~l~g~~i~v~~a~~~~  498 (661)
                                        |.|+.|.+++|..+|+++|||||+|.+.++|.+|+ .+++..|.|+.|.|...+.+.
T Consensus       303 ------------------g~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~  359 (549)
T KOG0147|consen  303 ------------------GKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERV  359 (549)
T ss_pred             ------------------ccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeec
Confidence                              78999999999999999999999999999999997 556689999999987765443

>KOG0124|consensus

Probab=99.75  E-value=4.6e-18  Score=167.34  Aligned_cols=177  Identities=19%  Similarity=0.392  Sum_probs=148.8

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      -|+|||+.|.+.+.|+.|+..|.+||+|++|.+..|+.|++++|||||+|+-+|.|+-|++.+ +..++||.|+|.....
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            489999999999999999999999999999999999999999999999999999999999998 5789999999963221


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCC
Q psy15852        263 KPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDV  342 (661)
Q Consensus       263 k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  342 (661)
                      -+.                                                                    ..|.     
T Consensus       193 mpQ--------------------------------------------------------------------AQpi-----  199 (544)
T KOG0124|consen  193 MPQ--------------------------------------------------------------------AQPI-----  199 (544)
T ss_pred             Ccc--------------------------------------------------------------------cchH-----
Confidence            110                                                                    0000     


Q ss_pred             CccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCCcc
Q psy15852        343 TGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTE  422 (661)
Q Consensus       343 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~  422 (661)
                                            ...-+++.|.|+             .+++....|++++++|+..|+.|          
T Consensus       200 ----------------------ID~vqeeAk~fn-------------RiYVaSvHpDLSe~DiKSVFEAF----------  234 (544)
T KOG0124|consen  200 ----------------------IDMVQEEAKKFN-------------RIYVASVHPDLSETDIKSVFEAF----------  234 (544)
T ss_pred             ----------------------HHHHHHHHHhhh-------------eEEeeecCCCccHHHHHHHHHhh----------
Confidence                                  011224444443             46777888999999999999998          


Q ss_pred             cchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHhCCC-CcCCCcEEEEecCCCCC
Q psy15852        423 HMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK-QKINDKEVDVKKATPKP  498 (661)
Q Consensus       423 ~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~~~~-~~l~g~~i~v~~a~~~~  498 (661)
                                          |+|..|.+.++...+..+||||++|.+..+-..|+..++ ..|.|..|+|.++...+
T Consensus       235 --------------------G~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP  291 (544)
T KOG0124|consen  235 --------------------GEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  291 (544)
T ss_pred             --------------------cceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccCCC
Confidence                                789999999999999999999999999999999996666 88999999998876554

>KOG0131|consensus

Probab=99.74  E-value=8.2e-18  Score=151.37  Aligned_cols=167  Identities=20%  Similarity=0.320  Sum_probs=141.6

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC-CccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK-QKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~-~~~~g~~i~V~~a~  261 (661)
                      ...+|||+||+..++++.|.++|-+.|+|.++++++|+.++..+|||||+|.++++|+-|++-++ ..+.|++|+|..+.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            45789999999999999999999999999999999999999999999999999999999999986 68999999999887


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccC
Q psy15852        262 PKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVD  341 (661)
Q Consensus       262 ~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (661)
                      ......                                                                          
T Consensus        88 ~~~~nl--------------------------------------------------------------------------   93 (203)
T KOG0131|consen   88 AHQKNL--------------------------------------------------------------------------   93 (203)
T ss_pred             cccccc--------------------------------------------------------------------------
Confidence            322110                                                                          


Q ss_pred             CCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCCc
Q psy15852        342 VTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTT  421 (661)
Q Consensus       342 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~  421 (661)
                                                                  .+.-++++.++.|.+++.-|...|+.|+        
T Consensus        94 --------------------------------------------~vganlfvgNLd~~vDe~~L~dtFsafG--------  121 (203)
T KOG0131|consen   94 --------------------------------------------DVGANLFVGNLDPEVDEKLLYDTFSAFG--------  121 (203)
T ss_pred             --------------------------------------------cccccccccccCcchhHHHHHHHHHhcc--------
Confidence                                                        1123466777778888888888888874        


Q ss_pred             ccchhhcccccccchhhccCCceeEEe-eecccccCCcccceEEEEeCChHHHHHHHhCC-CCcCCCcEEEEecCCCC
Q psy15852        422 EHMVLVTGTDMMHMEVTEAVPMEIIET-EMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  497 (661)
Q Consensus       422 ~~~~~~~~~~~~~~~~~~~~~G~i~~~-~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~~~-~~~l~g~~i~v~~a~~~  497 (661)
                                            .+... ++.+|..|+.++|||||.|.+.|.+.+|+..+ ++.+.+++|.|..+..+
T Consensus       122 ----------------------~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~  177 (203)
T KOG0131|consen  122 ----------------------VLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKK  177 (203)
T ss_pred             ----------------------ccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEec
Confidence                                  45544 57888999999999999999999999999554 47789999999998866

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.73  E-value=5.1e-17  Score=148.73  Aligned_cols=86  Identities=24%  Similarity=0.566  Sum_probs=79.4

Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                      ....++|||+|||+++++++|+++|++||.|.+|.|+.++.+++++|||||+|.+.++|++|++.+ +..|+|+.|+|.+
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            344689999999999999999999999999999999999999999999999999999999999876 6899999999999


Q ss_pred             ccCCCCC
Q psy15852        260 ATPKPEP  266 (661)
Q Consensus       260 a~~k~~~  266 (661)
                      +.++...
T Consensus       111 a~~~~~~  117 (144)
T PLN03134        111 ANDRPSA  117 (144)
T ss_pred             CCcCCCC
Confidence            9876543

>KOG0109|consensus

Probab=99.70  E-value=7.6e-17  Score=155.00  Aligned_cols=155  Identities=19%  Similarity=0.428  Sum_probs=133.8

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCC
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKP  264 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~  264 (661)
                      +|||+|||..+++.+|+.+|++||+|.+|.|+        |.||||..++...|..||..+ +.+|+|..|.|+.++.|.
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv--------KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIV--------KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeee--------cccceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            69999999999999999999999999999997        679999999999999999987 568999999999988763


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCCCc
Q psy15852        265 EPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTG  344 (661)
Q Consensus       265 ~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (661)
                      ..                                                                              
T Consensus        76 k~------------------------------------------------------------------------------   77 (346)
T KOG0109|consen   76 KA------------------------------------------------------------------------------   77 (346)
T ss_pred             CC------------------------------------------------------------------------------
Confidence            21                                                                              


Q ss_pred             cEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCCcccc
Q psy15852        345 VIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTEHM  424 (661)
Q Consensus       345 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~~~  424 (661)
                                                                 ...+.|.|..|..+..||++.|..++           
T Consensus        78 -------------------------------------------stkl~vgNis~tctn~ElRa~fe~yg-----------  103 (346)
T KOG0109|consen   78 -------------------------------------------STKLHVGNISPTCTNQELRAKFEKYG-----------  103 (346)
T ss_pred             -------------------------------------------ccccccCCCCccccCHHHhhhhcccC-----------
Confidence                                                       11244556667889999999999995           


Q ss_pred             hhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHH-hCCCCcCCCcEEEEecCCCCCCCCCC
Q psy15852        425 VLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL-KNPKQKINDKEVDVKKATPKPEPFGV  503 (661)
Q Consensus       425 ~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai-~~~~~~l~g~~i~v~~a~~~~~~~~~  503 (661)
                                         .|++|.|+.        +|+||+|+-.++|..|+ .+++..+.|+++.|..++++-....+
T Consensus       104 -------------------pviecdivk--------dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrtapg  156 (346)
T KOG0109|consen  104 -------------------PVIECDIVK--------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAPG  156 (346)
T ss_pred             -------------------Cceeeeeec--------ceeEEEEeeccchHHHHhcccccccccceeeeeeeccccccCCC
Confidence                               499999887        79999999999999999 67778999999999999988776665


Q ss_pred             CCCC
Q psy15852        504 RGGR  507 (661)
Q Consensus       504 ~~~~  507 (661)
                      .+..
T Consensus       157 mgDq  160 (346)
T KOG0109|consen  157 MGDQ  160 (346)
T ss_pred             CCCH
Confidence            5553

>KOG1190|consensus

Probab=99.65  E-value=4.8e-14  Score=141.65  Aligned_cols=224  Identities=14%  Similarity=0.153  Sum_probs=153.0

Q ss_pred             CCCCCceEEeCCCCCCCCcHHHHHHHh-hhccccccccEEeecCCCCceeeecccc------------ccccccc-----
Q psy15852         26 VKDDDRKLFCPLSSYLELDYLQLWQYF-DWVSSSFSENCLLEDSIGKPLTVSCSHH------------YYLFDQI-----   87 (661)
Q Consensus        26 ~~~~~r~lfVg~l~~~~te~~~l~~~F-~~g~~~~~~~~~~~d~~~~~~~~~~~~~------------~~l~~~~-----   87 (661)
                      ....-|-|.+++||++++| ++|.+++ .||  .+..+..++-.+-.-+..+..+.            .-|.++.     
T Consensus        24 ~~~pSkV~HlRnlp~e~tE-~elI~Lg~pFG--~vtn~~~lkGknQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~  100 (492)
T KOG1190|consen   24 MAEPSKVVHLRNLPWEVTE-EELISLGLPFG--KVTNLLMLKGKNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQY  100 (492)
T ss_pred             ccCCcceeEeccCCccccH-HHHHHhccccc--ceeeeeeeccchhhhhhhcchhhhhheeecccccCccccCcceeehh
Confidence            3345678999999999999 9999999 999  88888777764322211111100            0000000     


Q ss_pred             --------------ccceee---------------------eeecCCC---cEEEEcCCCcCCHHHHHHHhhcCCCeeEE
Q psy15852         88 --------------LRTHFF---------------------YIMEAKN---KMVSHPGIVHKITEELKEHFSKYGEIENV  129 (661)
Q Consensus        88 --------------~r~~~~---------------------~~~~~~~---~~~~~~~~~~~te~~L~~~F~~~G~I~~v  129 (661)
                                    .|....                     ...+..+   ++|+.....-++-+-|..+|++||.|..|
T Consensus       101 sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKI  180 (492)
T KOG1190|consen  101 SNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKI  180 (492)
T ss_pred             hhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEE
Confidence                          000000                     0000011   23334444589999999999999999877


Q ss_pred             EEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeeccee--ehhhhh----------hcc--------------
Q psy15852        130 TLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK--IEAKKA----------KAK--------------  183 (661)
Q Consensus       130 ~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~--i~v~~~----------~~~--------------  183 (661)
                      .-... + ...  -|.|+|.+.+.|..|    ...++|..|.+-.  +++.++          ..+              
T Consensus       181 iTF~K-n-n~F--QALvQy~d~~sAq~A----K~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~  252 (492)
T KOG1190|consen  181 ITFTK-N-NGF--QALVQYTDAVSAQAA----KLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDG  252 (492)
T ss_pred             EEEec-c-cch--hhhhhccchhhHHHH----HHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCcc
Confidence            55542 2 112  389999999999999    8888887664321  111111          100              


Q ss_pred             --------------------------------------------CCeeEecCCCc-cCCHHHHHHHHhcCCCeEEEEecc
Q psy15852        184 --------------------------------------------SGKIFVGGLSP-EMKDEEIKAHFAQFGNIIETEMPY  218 (661)
Q Consensus       184 --------------------------------------------~~~lfV~nLp~-~~te~~L~~~F~~~G~i~~v~i~~  218 (661)
                                                                  ...|.|.||-. .+|.+.|..+|+-||.|..|+|+.
T Consensus       253 ~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~  332 (492)
T KOG1190|consen  253 QPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILY  332 (492)
T ss_pred             ccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhcceEEEEeee
Confidence                                                        14578888865 499999999999999999999998


Q ss_pred             CCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCCC
Q psy15852        219 DKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKPE  265 (661)
Q Consensus       219 ~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~~  265 (661)
                      ++     +--|.|+|.+...|+-|+..+ ++.+.|++|+|.+++-..-
T Consensus       333 nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~v  375 (492)
T KOG1190|consen  333 NK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNV  375 (492)
T ss_pred             cC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccc
Confidence            65     345999999999999999998 7899999999999876543

>KOG0105|consensus

Probab=99.62  E-value=2.2e-14  Score=129.18  Aligned_cols=77  Identities=23%  Similarity=0.406  Sum_probs=68.3

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      .+++|||+|||.++.+.+|+++|.+||.|..|.+...   .....||||+|+++-+|+.||... +..++|..|+|+++.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            4589999999999999999999999999999998543   234789999999999999999886 678999999999975


Q ss_pred             C
Q psy15852        262 P  262 (661)
Q Consensus       262 ~  262 (661)
                      .
T Consensus        82 g   82 (241)
T KOG0105|consen   82 G   82 (241)
T ss_pred             C
Confidence            3

>KOG0105|consensus

Probab=99.58  E-value=3.9e-14  Score=127.65  Aligned_cols=148  Identities=17%  Similarity=0.333  Sum_probs=123.1

Q ss_pred             CCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         99 KNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        99 ~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ..+.||++|+| ++-+.+|+++|.+||.|.+|.|..-+   ..-.||||+|+++.+|+.|    |...++..+.|..|.|
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDA----iygRdGYdydg~rLRV   77 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDA----IYGRDGYDYDGCRLRV   77 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhh----hhcccccccCcceEEE
Confidence            34567777777 99999999999999999999987532   3457999999999999999    9999999999999999


Q ss_pred             hhhhcc-------------------------------CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcC
Q psy15852        178 KKAKAK-------------------------------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRK  226 (661)
Q Consensus       178 ~~~~~~-------------------------------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~  226 (661)
                      ..+..-                               ..+|.|++||++-+++||+++..+-|.|....+.+|       
T Consensus        78 Efprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------  150 (241)
T KOG0105|consen   78 EFPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------  150 (241)
T ss_pred             EeccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------
Confidence            876422                               157999999999999999999999999999988765       


Q ss_pred             cEEEEEeCCHHHHHHHHHhCC-C--ccCCeEEEEEec
Q psy15852        227 NFCFITFEHESVVIDLLKNPK-Q--KINDKEVDVKKA  260 (661)
Q Consensus       227 g~afV~f~~~~~A~~Al~~~~-~--~~~g~~i~V~~a  260 (661)
                      |++.|+|...|+..-|+..+. .  .-.|....+..-
T Consensus       151 g~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yirv~  187 (241)
T KOG0105|consen  151 GVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIRVR  187 (241)
T ss_pred             cceeeeeeehhhHHHHHHhhccccccCcCcEeeEEec
Confidence            478999999999999998872 2  225555444443

>KOG1365|consensus

Probab=99.50  E-value=2e-14  Score=142.94  Aligned_cols=281  Identities=15%  Similarity=0.103  Sum_probs=180.7

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKP  264 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k~  264 (661)
                      .-+..++||+..++.+|..+|.-.-...--..+.....|+..|.+.|.|.+.|.-+.|++...+.+.++.|.|-.+....
T Consensus        61 vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~ge~  140 (508)
T KOG1365|consen   61 VVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKATGEE  140 (508)
T ss_pred             eEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccCchh
Confidence            34667899999999999999975322111111222223777899999999999999999999888999999998876543


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCCCc
Q psy15852        265 EPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTG  344 (661)
Q Consensus       265 ~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (661)
                      .-.                                +.++.                    .+..+.              
T Consensus       141 f~~--------------------------------iagg~--------------------s~e~~~--------------  154 (508)
T KOG1365|consen  141 FLK--------------------------------IAGGT--------------------SNEAAP--------------  154 (508)
T ss_pred             heE--------------------------------ecCCc--------------------cccCCC--------------
Confidence            210                                00000                    000000              


Q ss_pred             cEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCC-cCccchhhhhhccCcccccCCccc
Q psy15852        345 VIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPS-IRELEIPEAFLTKTTTVPMTTTEH  423 (661)
Q Consensus       345 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~-~~~~~l~~~f~~~~~~~~~~~~~~  423 (661)
                                                    |..+        -.-+++.-..+|. .++.++.++|.+.++..       
T Consensus       155 ------------------------------flsk--------~~qvivRmRGLPfdat~~dVv~FF~~~cpv~-------  189 (508)
T KOG1365|consen  155 ------------------------------FLSK--------ENQVIVRMRGLPFDATALDVVEFFGPPCPVT-------  189 (508)
T ss_pred             ------------------------------CCCc--------ccceEEEecCCCCCcchHHHHHhcCCCCccc-------
Confidence                                          0000        0012222334565 88888888887554310       


Q ss_pred             chhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHhCCCCcCCCcEEEEecCCCCCCCC--
Q psy15852        424 MVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEPF--  501 (661)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~~~~~~l~g~~i~v~~a~~~~~~~--  501 (661)
                                         |-.+.+-. ..+.+|+..|-|||.|..+++|+.|+..+.+.|+-|.|++-+++..+..+  
T Consensus       190 -------------------~g~egvLF-V~rpdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFRSTaaEvqqvl  249 (508)
T KOG1365|consen  190 -------------------GGTEGVLF-VTRPDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFRSTAAEVQQVL  249 (508)
T ss_pred             -------------------CCccceEE-EECCCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHHHhHHHHHHHH
Confidence                               11222222 22456788899999999999999999999999999999987776554221  


Q ss_pred             --CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCccccccccccCCCCCcccCCCcccccc
Q psy15852        502 --GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFD  579 (661)
Q Consensus       502 --~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~  579 (661)
                        ..+.+-.+.-     +    .                                        ..-|.      .+..  
T Consensus       250 nr~~s~pLi~~~-----~----s----------------------------------------p~~p~------~p~~--  272 (508)
T KOG1365|consen  250 NREVSEPLIPGL-----T----S----------------------------------------PLLPG------GPAR--  272 (508)
T ss_pred             HhhccccccCCC-----C----C----------------------------------------CCCCC------Cccc--
Confidence              0000000000     0    0                                        00000      0000  


Q ss_pred             CCCCccccccccCCCeEEEcCCCCCCCHHHHHHHhhcCCC-eeE--EEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        580 QNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGE-IEN--VTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       580 ~~~~~~~~~~~~~~~~l~v~nlp~~~te~dL~~~F~~~G~-I~~--v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                            .+.....+.+|-.|+||++++.+||-++|..|-. |..  |+++.+.. |++.|.|||+|.+.|+|.+|+.+-|
T Consensus       273 ------~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~q-GrPSGeAFIqm~nae~a~aaaqk~h  345 (508)
T KOG1365|consen  273 ------LVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQ-GRPSGEAFIQMRNAERARAAAQKCH  345 (508)
T ss_pred             ------cCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCC-CCcChhhhhhhhhhHHHHHHHHHHH
Confidence                  0111223678999999999999999999999864 444  89999887 9999999999999999999999876


Q ss_pred             cccC
Q psy15852        657 YFYS  660 (661)
Q Consensus       657 ~~~~  660 (661)
                      --||
T Consensus       346 k~~m  349 (508)
T KOG1365|consen  346 KKLM  349 (508)
T ss_pred             Hhhc
Confidence            5554

>KOG0149|consensus

Probab=99.50  E-value=3e-14  Score=134.11  Aligned_cols=64  Identities=30%  Similarity=0.517  Sum_probs=61.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      -+||||++|||+++.++|+++|.+||+|+++.|+.|+.||||||||||+|.+.+.|++|++.-+
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~   75 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN   75 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC
Confidence            4799999999999999999999999999999999999999999999999999999999998643

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.49  E-value=9.6e-14  Score=127.12  Aligned_cols=80  Identities=24%  Similarity=0.415  Sum_probs=71.9

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..+++|.+|+++++|++|+++|++||+|.+|+|+.++.|+++||||||+|.++++|++|    +..+++..|.|++|.|.
T Consensus        34 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~A----l~~lng~~i~Gr~l~V~  109 (144)
T PLN03134         34 STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAA----ISEMDGKELNGRHIRVN  109 (144)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHH----HHHcCCCEECCEEEEEE
Confidence            34555555555999999999999999999999999999999999999999999999999    88899999999999998


Q ss_pred             hhhc
Q psy15852        179 KAKA  182 (661)
Q Consensus       179 ~~~~  182 (661)
                      ++.+
T Consensus       110 ~a~~  113 (144)
T PLN03134        110 PAND  113 (144)
T ss_pred             eCCc
Confidence            8754

>KOG4206|consensus

Probab=99.45  E-value=1.1e-12  Score=123.41  Aligned_cols=148  Identities=24%  Similarity=0.335  Sum_probs=124.5

Q ss_pred             EEEEcCCC-cCCHHHHHH----HhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852        102 MVSHPGIV-HKITEELKE----HFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus       102 ~~~~~~~~-~~te~~L~~----~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ++|+.|+. .+..++|+.    +|++||.|.+|...+   |.+.||-|||.|.+.+.|..|    ...++|..+.|+++.
T Consensus        11 TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A----~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen   11 TLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAA----LRALQGFPFYGKPMR   83 (221)
T ss_pred             eEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHH----HHHhcCCcccCchhh
Confidence            77888887 788888777    999999999998876   478999999999999999999    889999999999999


Q ss_pred             hhhhhccC-------------------------------------------------------CeeEecCCCccCCHHHH
Q psy15852        177 AKKAKAKS-------------------------------------------------------GKIFVGGLSPEMKDEEI  201 (661)
Q Consensus       177 v~~~~~~~-------------------------------------------------------~~lfV~nLp~~~te~~L  201 (661)
                      +.++..++                                                       ..+|+.|||..++.+.|
T Consensus        84 iqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l  163 (221)
T KOG4206|consen   84 IQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEML  163 (221)
T ss_pred             eecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHH
Confidence            88875332                                                       35899999999999999


Q ss_pred             HHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccC-CeEEEEEecc
Q psy15852        202 KAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIN-DKEVDVKKAT  261 (661)
Q Consensus       202 ~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~-g~~i~V~~a~  261 (661)
                      ..+|.+|.-...|+++...     ++.|||+|.+...|..|...+ +..+- ...+.|.++.
T Consensus       164 ~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  164 SDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            9999999989999887542     789999999998888888876 33332 6677776653

>KOG4307|consensus

Probab=99.42  E-value=4.7e-12  Score=134.80  Aligned_cols=156  Identities=10%  Similarity=0.070  Sum_probs=116.6

Q ss_pred             EEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhh
Q psy15852        102 MVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAK  181 (661)
Q Consensus       102 ~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~  181 (661)
                      +-|.+-..+.++.+++++|... .|-.+.|..+...+...|-++|+|....++.+|     ...|....-.|.+.+..+-
T Consensus       314 ~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A-----~~rn~~~~~~R~~q~~P~g  387 (944)
T KOG4307|consen  314 NNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNA-----FTRNPSDDVNRPFQTGPPG  387 (944)
T ss_pred             eeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHH-----HhcCchhhhhcceeecCCC
Confidence            3444555689999999998653 366777777665444588999999999999996     4455555555666554321


Q ss_pred             cc--------------------------------------------CCeeEecCCCccCCHHHHHHHHhcCCCeEE-EEe
Q psy15852        182 AK--------------------------------------------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIE-TEM  216 (661)
Q Consensus       182 ~~--------------------------------------------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~-v~i  216 (661)
                      ..                                            ..+|||..||..+++.++-++|..--.|++ |.|
T Consensus       388 ~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~l  467 (944)
T KOG4307|consen  388 NLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIEL  467 (944)
T ss_pred             ccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEe
Confidence            10                                            058999999999999999999999777776 666


Q ss_pred             ccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCC
Q psy15852        217 PYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKP  264 (661)
Q Consensus       217 ~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~  264 (661)
                      .+-+ +++.++.|||.|..++++.+|+... .+++..+.|+|.....+.
T Consensus       468 t~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~~  515 (944)
T KOG4307|consen  468 TRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADYA  515 (944)
T ss_pred             ccCC-cccccchhhheeccccccchhhhcccccccCceEEEeechhhHH
Confidence            5544 4778999999999988888887665 577888999998765543

>KOG0149|consensus

Probab=99.41  E-value=3e-13  Score=127.44  Aligned_cols=79  Identities=32%  Similarity=0.536  Sum_probs=75.6

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      -.+|||++|++.+..+.|+++|++||+|.++.|+.|+.+|++|||+||+|.+.++|.+|++..+..|+||+..+..|.-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhhh
Confidence            3689999999999999999999999999999999999999999999999999999999999999999999999988764

>KOG1548|consensus

Probab=99.38  E-value=8.6e-12  Score=123.44  Aligned_cols=164  Identities=18%  Similarity=0.268  Sum_probs=136.6

Q ss_pred             eeeeecCCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeE--------EEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHH
Q psy15852         92 FFYIMEAKNKMVSHPGIV-HKITEELKEHFSKYGEIEN--------VTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  162 (661)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~--------v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~  162 (661)
                      |....+..++.|||.++| ++|.+++.++|++||.|.+        |+|.++.+ |+.||=|.|.|-..+++..|    +
T Consensus       126 ~~~~~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA----~  200 (382)
T KOG1548|consen  126 WFNPEPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELA----I  200 (382)
T ss_pred             ccCcccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHH----H
Confidence            444445567778888888 9999999999999998754        78999876 99999999999999999999    9


Q ss_pred             HHhCCeeecceeehhhhhhcc-------------------------------------------CCeeEecCCCc----c
Q psy15852        163 IAEGNHVINNKKIEAKKAKAK-------------------------------------------SGKIFVGGLSP----E  195 (661)
Q Consensus       163 ~~~~~~~i~g~~i~v~~~~~~-------------------------------------------~~~lfV~nLp~----~  195 (661)
                      ..|++..+.|+.|+|..|+-.                                           .++|.++|+-.    .
T Consensus       201 ~ilDe~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~  280 (382)
T KOG1548|consen  201 KILDEDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFE  280 (382)
T ss_pred             HHhCcccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhc
Confidence            999999999999999876311                                           16799999832    2


Q ss_pred             CC-------HHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCC
Q psy15852        196 MK-------DEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKP  264 (661)
Q Consensus       196 ~t-------e~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~  264 (661)
                      .+       +++|++-+++||.|..|.|.-    .++.|.+-|.|.+.++|..||+.| +..+.||.|.......+.
T Consensus       281 ~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~t  353 (382)
T KOG1548|consen  281 KNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGKT  353 (382)
T ss_pred             cCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCcc
Confidence            22       357788899999999998753    456899999999999999999998 789999999988766544

>KOG0122|consensus

Probab=99.38  E-value=7.6e-13  Score=125.02  Aligned_cols=67  Identities=27%  Similarity=0.419  Sum_probs=63.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ..++|-|.||+-+++|+||++||.+||.|.+|.|.+|+.||.+||||||+|.+.++|.+||+.++.+
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~  254 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGY  254 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCc
Confidence            3578999999999999999999999999999999999999999999999999999999999987654

>PF00076 RRM_1: RNA recognition motif

Probab=99.38  E-value=9.8e-13  Score=105.09  Aligned_cols=62  Identities=32%  Similarity=0.494  Sum_probs=58.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        596 MVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       596 l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      |||+|||+++|+++|+++|++||.|..+++..+ .+++++|+|||+|.+.++|++|++.++..
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~   62 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGK   62 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCC
Confidence            799999999999999999999999999999998 56999999999999999999999976654

(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 ....

>KOG0120|consensus

Probab=99.37  E-value=4.4e-12  Score=134.89  Aligned_cols=152  Identities=22%  Similarity=0.385  Sum_probs=125.8

Q ss_pred             cEEEEcCCC-cCCHHHHHHHhhcC-----------CC-eeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCC
Q psy15852        101 KMVSHPGIV-HKITEELKEHFSKY-----------GE-IENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGN  167 (661)
Q Consensus       101 ~~~~~~~~~-~~te~~L~~~F~~~-----------G~-I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~  167 (661)
                      .-+++.+++ .++++.+-.+|..-           |+ |..|.+-..++      |||++|.+.++|..     ++.+++
T Consensus       176 ~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~n------fa~ie~~s~~~at~-----~~~~~~  244 (500)
T KOG0120|consen  176 RRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEKN------FAFIEFRSISEATE-----AMALDG  244 (500)
T ss_pred             hhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeeccccc------ceeEEecCCCchhh-----hhcccc
Confidence            345666665 89999999999764           54 77777766544      99999999999999     577778


Q ss_pred             eeecceeehhhhhhc----------------------------cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccC
Q psy15852        168 HVINNKKIEAKKAKA----------------------------KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYD  219 (661)
Q Consensus       168 ~~i~g~~i~v~~~~~----------------------------~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~  219 (661)
                      ..+.|+++.+.....                            ...++||++||..+++.+++++...||.+....++.+
T Consensus       245 ~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d  324 (500)
T KOG0120|consen  245 IIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKD  324 (500)
T ss_pred             hhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecc
Confidence            777777765533210                            0167999999999999999999999999999999999


Q ss_pred             CCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        220 KSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       220 ~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ..+|.++||||.+|.+......|+..+ +..+.++.|.|..|-.-
T Consensus       325 ~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g  369 (500)
T KOG0120|consen  325 SATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVG  369 (500)
T ss_pred             cccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhcc
Confidence            999999999999999999999999998 56788899999888753

>KOG0121|consensus

Probab=99.36  E-value=2.2e-12  Score=109.64  Aligned_cols=94  Identities=23%  Similarity=0.342  Sum_probs=82.7

Q ss_pred             cceeehhhhhhccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCc
Q psy15852        171 NNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQK  249 (661)
Q Consensus       171 ~g~~i~v~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~  249 (661)
                      .|.......+..++++|||+||++.++|++|.++|+++|+|..|.+-.|+.+..+.|||||+|.+.++|..||+-. +..
T Consensus        23 ~gt~~e~~~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryisgtr  102 (153)
T KOG0121|consen   23 RGTDEEQLEALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTR  102 (153)
T ss_pred             cCchHHHHHHHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCc
Confidence            3344444556677899999999999999999999999999999999999998999999999999999999999997 688


Q ss_pred             cCCeEEEEEeccCCC
Q psy15852        250 INDKEVDVKKATPKP  264 (661)
Q Consensus       250 ~~g~~i~V~~a~~k~  264 (661)
                      ++.++|.|.|...-.
T Consensus       103 Lddr~ir~D~D~GF~  117 (153)
T KOG0121|consen  103 LDDRPIRIDWDAGFV  117 (153)
T ss_pred             ccccceeeeccccch
Confidence            999999999876543

>KOG0120|consensus

Probab=99.33  E-value=1.6e-11  Score=130.75  Aligned_cols=160  Identities=19%  Similarity=0.341  Sum_probs=127.3

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+++++.+++-..++.++.++...||++....++.+..+|.++||||.+|.++--...|    +..+||..+.++++.|.
T Consensus       289 ~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A----~agLnGm~lgd~~lvvq  364 (500)
T KOG0120|consen  289 PNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQA----IAGLNGMQLGDKKLVVQ  364 (500)
T ss_pred             cchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhh----hcccchhhhcCceeEee
Confidence            34455555555999999999999999999999999999999999999999999999999    99999999999999888


Q ss_pred             hhhccCCe-----------------------------eEecCC--CccC-CH-------HHHHHHHhcCCCeEEEEeccC
Q psy15852        179 KAKAKSGK-----------------------------IFVGGL--SPEM-KD-------EEIKAHFAQFGNIIETEMPYD  219 (661)
Q Consensus       179 ~~~~~~~~-----------------------------lfV~nL--p~~~-te-------~~L~~~F~~~G~i~~v~i~~~  219 (661)
                      .+......                             |.+.|+  |.++ ++       |+++.-+++||.|..|.+++.
T Consensus       365 ~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~  444 (500)
T KOG0120|consen  365 RAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRP  444 (500)
T ss_pred             hhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCC
Confidence            77543211                             111111  1111 11       466777899999999999987


Q ss_pred             -CC--CCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        220 -KS--KSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       220 -~~--~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                       ..  -....|-.||+|.+.+++++|++++ |.++.+|.|...+...
T Consensus       445 ~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  445 YPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             CCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence             21  1344567899999999999999999 7899999999888654

>KOG0122|consensus

Probab=99.33  E-value=3.9e-12  Score=120.28  Aligned_cols=81  Identities=22%  Similarity=0.398  Sum_probs=76.4

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|.|.||+.++++++|+++|.+||.|..|.|.+|+.||.++|||||.|.+.++|++||+.+ ++-++.-.|.|.|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            3478999999999999999999999999999999999999999999999999999999999998 577888899999998


Q ss_pred             CC
Q psy15852        262 PK  263 (661)
Q Consensus       262 ~k  263 (661)
                      |+
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            85

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.31  E-value=5.7e-12  Score=100.83  Aligned_cols=60  Identities=30%  Similarity=0.473  Sum_probs=56.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        596 MVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       596 l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      |||+|||+.++++||+++|+.||.|..|++..++. |+++|+|||+|.++++|.+|+...+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~   60 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLN   60 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCC
Confidence            79999999999999999999999999999999988 9999999999999999999999877

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 ....

>KOG0107|consensus

Probab=99.31  E-value=1.2e-11  Score=111.33  Aligned_cols=77  Identities=21%  Similarity=0.432  Sum_probs=70.7

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      .++|||+||+..+++.||+..|..||+|.+|+|.+.     +.|||||+|+++.+|..|+..| +..|+|..|.|+...-
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            578999999999999999999999999999999865     4899999999999999999998 6899999999999876


Q ss_pred             CCC
Q psy15852        263 KPE  265 (661)
Q Consensus       263 k~~  265 (661)
                      +..
T Consensus        85 ~~r   87 (195)
T KOG0107|consen   85 RPR   87 (195)
T ss_pred             Ccc
Confidence            554

>PF00076 RRM_1: RNA recognition motif

Probab=99.29  E-value=1.3e-11  Score=98.49  Aligned_cols=69  Identities=32%  Similarity=0.547  Sum_probs=62.1

Q ss_pred             EEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852        103 VSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus       103 ~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ++.++++++++++|+++|++||+|..+.++.+ .+++++|||||+|.+.++|++|    +..+++..+.|++|+
T Consensus         2 ~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a----~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    2 YVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKA----LEELNGKKINGRKIR   70 (70)
T ss_dssp             EEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHH----HHHHTTEEETTEEEE
T ss_pred             EEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHH----HHHcCCCEECccCcC
Confidence            44445559999999999999999999999997 5689999999999999999999    888999999999874

(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

Probab=99.29  E-value=3.3e-12  Score=121.78  Aligned_cols=137  Identities=22%  Similarity=0.421  Sum_probs=118.1

Q ss_pred             EEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhh
Q psy15852        102 MVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAK  181 (661)
Q Consensus       102 ~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~  181 (661)
                      +++..+++.+.+.+|..+|..||.|.+|.+..        ||+||+|.+..+|..|    +..+++..|.+..+.+.++.
T Consensus         4 v~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Da----v~~l~~~~l~~e~~vve~~r   71 (216)
T KOG0106|consen    4 VYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDA----VHDLDGKELCGERLVVEHAR   71 (216)
T ss_pred             eeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcc----cchhcCceecceeeeeeccc
Confidence            44455555999999999999999999998865        5999999999999999    99999999999887777765


Q ss_pred             cc-------------------------CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCH
Q psy15852        182 AK-------------------------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE  236 (661)
Q Consensus       182 ~~-------------------------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~  236 (661)
                      ..                         .+.|+|.+++..+.+.+|.+.|+++|.+....+        ..+++||+|.+.
T Consensus        72 ~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~  143 (216)
T KOG0106|consen   72 GKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQ  143 (216)
T ss_pred             ccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhh
Confidence            21                         167999999999999999999999999855544        367899999999


Q ss_pred             HHHHHHHHhC-CCccCCeEEEEE
Q psy15852        237 SVVIDLLKNP-KQKINDKEVDVK  258 (661)
Q Consensus       237 ~~A~~Al~~~-~~~~~g~~i~V~  258 (661)
                      ++|.+|+..+ +..+.++.|.+.
T Consensus       144 ~da~ra~~~l~~~~~~~~~l~~~  166 (216)
T KOG0106|consen  144 EDAKRALEKLDGKKLNGRRISVE  166 (216)
T ss_pred             hhhhhcchhccchhhcCceeeec
Confidence            9999999998 688999999993

>KOG4207|consensus

Probab=99.27  E-value=1.1e-11  Score=113.99  Aligned_cols=79  Identities=19%  Similarity=0.373  Sum_probs=74.9

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ..|.|-||-+-++.++|+.+|++||.|-+|.|++|+-|+.++|||||.|....+|+.|+++| +..|+|+.|.|++|.--
T Consensus        14 ~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~aryg   93 (256)
T KOG4207|consen   14 TSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARYG   93 (256)
T ss_pred             eeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhcC
Confidence            57999999999999999999999999999999999999999999999999999999999998 68999999999988643

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.27  E-value=2.1e-11  Score=119.45  Aligned_cols=78  Identities=22%  Similarity=0.290  Sum_probs=71.3

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK  263 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k  263 (661)
                      .++|||+|||+.+++++|+++|+.||+|.+|.|+++..   .+|||||+|.++++|..||..++..|.|+.|.|.++..-
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccCC
Confidence            36899999999999999999999999999999998854   479999999999999999987789999999999998754


Q ss_pred             C
Q psy15852        264 P  264 (661)
Q Consensus       264 ~  264 (661)
                      .
T Consensus        81 ~   81 (260)
T PLN03120         81 Q   81 (260)
T ss_pred             C
Confidence            3

>KOG4206|consensus

Probab=99.26  E-value=1.8e-10  Score=108.70  Aligned_cols=78  Identities=19%  Similarity=0.417  Sum_probs=70.7

Q ss_pred             CeeEecCCCccCCHHHHHH----HHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        185 GKIFVGGLSPEMKDEEIKA----HFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~----~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                      .+|||.||...+..++|+.    +|++||.|.+|...+   +.+.+|-|||.|.+.+.|-.|+..+ |.-+.|+.++|.+
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqy   86 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQY   86 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheec
Confidence            4999999999999999888    999999999998865   4677999999999999999999998 7899999999999


Q ss_pred             ccCCCC
Q psy15852        260 ATPKPE  265 (661)
Q Consensus       260 a~~k~~  265 (661)
                      |..+..
T Consensus        87 A~s~sd   92 (221)
T KOG4206|consen   87 AKSDSD   92 (221)
T ss_pred             ccCccc
Confidence            987653

>KOG0125|consensus

Probab=99.24  E-value=1.2e-11  Score=121.60  Aligned_cols=98  Identities=16%  Similarity=0.405  Sum_probs=82.7

Q ss_pred             HhCCeeecceeehhhhhh-----ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHH
Q psy15852        164 AEGNHVINNKKIEAKKAK-----AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESV  238 (661)
Q Consensus       164 ~~~~~~i~g~~i~v~~~~-----~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~  238 (661)
                      ..++....|..+.+....     ...++|+|+|||+...|-||+.+|.+||+|.+|.|+.+.  .-+|||+||+|++.++
T Consensus        71 ~~~~~~t~g~~~~~~~st~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~d  148 (376)
T KOG0125|consen   71 TSNGAPTDGQPIQTQPSTNSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPAD  148 (376)
T ss_pred             ccCCCCCCCCccccCCCCcCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhh
Confidence            344555566666665543     234899999999999999999999999999999999765  4479999999999999


Q ss_pred             HHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        239 VIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       239 A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      |++|-+++ +..+.||+|+|..|..+
T Consensus       149 adRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  149 ADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             HHHHHHHhhcceeeceEEEEeccchh
Confidence            99999998 68999999999998875

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.21  E-value=7.5e-11  Score=94.31  Aligned_cols=69  Identities=29%  Similarity=0.513  Sum_probs=60.6

Q ss_pred             EEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852        103 VSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus       103 ~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ++.++++++++++|+++|+.||.|..|++..+++ +.++|+|||+|.++++|.+|    +...++..+.|+.|+
T Consensus         2 ~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~a----l~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    2 YISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRA----LELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHH----HHHHTTEEETTEEEE
T ss_pred             EEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHH----HHHCCCcEECCEEcC
Confidence            4555556999999999999999999999999987 99999999999999999998    888888999999874

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 ....

>KOG0114|consensus

Probab=99.20  E-value=3.4e-11  Score=98.60  Aligned_cols=65  Identities=23%  Similarity=0.337  Sum_probs=59.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcccC
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFYS  660 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~~~  660 (661)
                      .+-|||+|||+++|.+|+.++|.+||.|.-|+|=..+   ..+|.|||.|++..+|.+|++++..|+.
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~   82 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNV   82 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhccccc
Confidence            4679999999999999999999999999999998765   4689999999999999999999888764

>KOG0113|consensus

Probab=99.20  E-value=1.6e-10  Score=112.46  Aligned_cols=80  Identities=23%  Similarity=0.440  Sum_probs=75.0

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ++|||.-|+++++|..|+..|+.||+|+.|.|+++..||+++|||||+|+++-+..+|.+.- +.+|+|+.|.|.+-..+
T Consensus       102 ~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvERgR  181 (335)
T KOG0113|consen  102 KTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVERGR  181 (335)
T ss_pred             ceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEecccc
Confidence            89999999999999999999999999999999999999999999999999999999999876 78999999999876554


Q ss_pred             C
Q psy15852        264 P  264 (661)
Q Consensus       264 ~  264 (661)
                      .
T Consensus       182 T  182 (335)
T KOG0113|consen  182 T  182 (335)
T ss_pred             c
Confidence            4

>KOG0121|consensus

Probab=99.20  E-value=2.9e-11  Score=102.90  Aligned_cols=78  Identities=21%  Similarity=0.293  Sum_probs=70.5

Q ss_pred             CCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         99 KNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        99 ~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      +.+++||+|+. .++||+|.++|+++|+|..|.+-.|+.+....|||||+|.+.++|+.|    +.-+++..++.++|.+
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~A----lryisgtrLddr~ir~  110 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDA----LRYISGTRLDDRPIRI  110 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHH----HHHhccCcccccceee
Confidence            34566666665 999999999999999999999999999999999999999999999999    8999999999999988


Q ss_pred             hhh
Q psy15852        178 KKA  180 (661)
Q Consensus       178 ~~~  180 (661)
                      .|-
T Consensus       111 D~D  113 (153)
T KOG0121|consen  111 DWD  113 (153)
T ss_pred             ecc
Confidence            764

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.18  E-value=1.7e-10  Score=118.20  Aligned_cols=131  Identities=31%  Similarity=0.511  Sum_probs=107.7

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.+|++++++++|+++|.+||+|..|.+..++.+++++|||||+|.++++|..|    +..+++..+.|++|.|.+
T Consensus       116 ~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a----~~~~~~~~~~~~~~~v~~  191 (306)
T COG0724         116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKA----IEELNGKELEGRPLRVQK  191 (306)
T ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHH----HHHcCCCeECCceeEeec
Confidence            4555555555999999999999999999999999988899999999999999999999    999999999999999988


Q ss_pred             hhc----c-------------------------CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEE
Q psy15852        180 AKA----K-------------------------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCF  230 (661)
Q Consensus       180 ~~~----~-------------------------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~af  230 (661)
                      ...    .                         ...+++.+++..++..++...|..+|.+..+.+.............+
T Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  271 (306)
T COG0724         192 AQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSF  271 (306)
T ss_pred             cccccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccc
Confidence            431    0                         15789999999999999999999999997777766544333333333


Q ss_pred             EEeC
Q psy15852        231 ITFE  234 (661)
Q Consensus       231 V~f~  234 (661)
                      +.+.
T Consensus       272 ~~~~  275 (306)
T COG0724         272 VGNE  275 (306)
T ss_pred             cchh
Confidence            3333

>KOG0125|consensus

Probab=99.16  E-value=4e-11  Score=117.84  Aligned_cols=80  Identities=23%  Similarity=0.406  Sum_probs=72.0

Q ss_pred             CCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852         98 AKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus        98 ~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ...+-++|.|+| ..-|.||+.+|.+||+|.+|.|+.+.  .-||||+||+|++++||++|    -.++++..|.||+|+
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRA----Ra~LHgt~VEGRkIE  167 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRA----RAELHGTVVEGRKIE  167 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHH----HHHhhcceeeceEEE
Confidence            345677888887 99999999999999999999999874  46999999999999999999    899999999999999


Q ss_pred             hhhhhcc
Q psy15852        177 AKKAKAK  183 (661)
Q Consensus       177 v~~~~~~  183 (661)
                      |..+..+
T Consensus       168 Vn~ATar  174 (376)
T KOG0125|consen  168 VNNATAR  174 (376)
T ss_pred             Eeccchh
Confidence            9988654

>KOG0113|consensus

Probab=99.16  E-value=6.9e-11  Score=114.87  Aligned_cols=80  Identities=23%  Similarity=0.403  Sum_probs=74.2

Q ss_pred             cCCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852         97 EAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus        97 ~~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ++-.|+||..|..+++|..|+..|+.||+|+.|+|++|+.||+++|||||+|.++.+...|    ....++..|+|+.|.
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~A----YK~adG~~Idgrri~  174 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAA----YKDADGIKIDGRRIL  174 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHH----HHhccCceecCcEEE
Confidence            5567889999999999999999999999999999999999999999999999999999999    888899999999887


Q ss_pred             hhhh
Q psy15852        177 AKKA  180 (661)
Q Consensus       177 v~~~  180 (661)
                      |..-
T Consensus       175 VDvE  178 (335)
T KOG0113|consen  175 VDVE  178 (335)
T ss_pred             EEec
Confidence            7643

>KOG0126|consensus

Probab=99.14  E-value=5e-12  Score=114.05  Aligned_cols=87  Identities=24%  Similarity=0.308  Sum_probs=74.5

Q ss_pred             ceeeeeecCCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCee
Q psy15852         90 THFFYIMEAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV  169 (661)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~  169 (661)
                      .+|...-..+.-+++++++.+.||.||...|++||+|.+|.|++|+.||+|+||||+.|++..+...|    +..+||..
T Consensus        26 ~SWH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILA----VDN~NGik  101 (219)
T KOG0126|consen   26 KSWHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILA----VDNLNGIK  101 (219)
T ss_pred             cchhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEE----EeccCCce
Confidence            34554444444455555555999999999999999999999999999999999999999999999999    99999999


Q ss_pred             ecceeehhhhh
Q psy15852        170 INNKKIEAKKA  180 (661)
Q Consensus       170 i~g~~i~v~~~  180 (661)
                      |.||.|+|...
T Consensus       102 i~gRtirVDHv  112 (219)
T KOG0126|consen  102 ILGRTIRVDHV  112 (219)
T ss_pred             ecceeEEeeec
Confidence            99999998754

>KOG0126|consensus

Probab=99.14  E-value=7.1e-12  Score=113.07  Aligned_cols=80  Identities=28%  Similarity=0.524  Sum_probs=74.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      .+..|||+|||+.+||.||..+|++||+|.+|.+++|+.||+++||||++|++.-+..-|+..+ +..|.||.|+|....
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            3568999999999999999999999999999999999999999999999999999988888887 689999999998654


Q ss_pred             C
Q psy15852        262 P  262 (661)
Q Consensus       262 ~  262 (661)
                      .
T Consensus       114 ~  114 (219)
T KOG0126|consen  114 N  114 (219)
T ss_pred             c
Confidence            4

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.13  E-value=2e-10  Score=110.70  Aligned_cols=77  Identities=17%  Similarity=0.208  Sum_probs=70.6

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKP  264 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k~  264 (661)
                      .+|||+||++.+|+++|+++|+.||+|.+|+|+++.   ..++||||+|.++++|..|+...+..|.+++|.|..+....
T Consensus         6 ~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~y~   82 (243)
T PLN03121          6 YTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQYE   82 (243)
T ss_pred             eEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcccc
Confidence            589999999999999999999999999999999884   44689999999999999999888999999999999877543

>KOG0130|consensus

Probab=99.13  E-value=1.3e-10  Score=99.70  Aligned_cols=82  Identities=21%  Similarity=0.343  Sum_probs=77.2

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC-CccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK-QKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~-~~~~g~~i~V~~a~~k  263 (661)
                      .-|||.++-...++++|.+.|..||+|+++.+..|+.||..+|||+|+|++.+.|++|+..++ ..|.|+.|.|.|+..+
T Consensus        73 wIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~  152 (170)
T KOG0130|consen   73 WIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVK  152 (170)
T ss_pred             EEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEec
Confidence            569999999999999999999999999999999999999999999999999999999999985 8999999999999876


Q ss_pred             CCC
Q psy15852        264 PEP  266 (661)
Q Consensus       264 ~~~  266 (661)
                      ...
T Consensus       153 gp~  155 (170)
T KOG0130|consen  153 GPE  155 (170)
T ss_pred             CCc
Confidence            543

>KOG1457|consensus

Probab=99.13  E-value=4.6e-10  Score=104.64  Aligned_cols=141  Identities=16%  Similarity=0.213  Sum_probs=109.3

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeC-CCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeec---ce
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSD-PNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVIN---NK  173 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~-~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~---g~  173 (661)
                      .-+++||.+|+-++.-.||..+|..|--.+.+.|... +...-.+-+|||.|.+..+|.+|    ...+||..++   +.
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aa----mnaLNGvrFDpE~~s  108 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAA----MNALNGVRFDPETGS  108 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHH----HHHhcCeeeccccCc
Confidence            3578888888889999999999999976777777653 22223568999999999999999    8999999885   45


Q ss_pred             eehhhhhhccC---------------------------------------------------------------------
Q psy15852        174 KIEAKKAKAKS---------------------------------------------------------------------  184 (661)
Q Consensus       174 ~i~v~~~~~~~---------------------------------------------------------------------  184 (661)
                      .+++..++...                                                                     
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            55555443211                                                                     


Q ss_pred             ----------------------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHH
Q psy15852        185 ----------------------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDL  242 (661)
Q Consensus       185 ----------------------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A  242 (661)
                                            .+|||-||..+++|++|+.+|+.|-....++|.-.    .....||++|++.+.|..|
T Consensus       189 ~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~----~g~~vaf~~~~~~~~at~a  264 (284)
T KOG1457|consen  189 KAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR----GGMPVAFADFEEIEQATDA  264 (284)
T ss_pred             cCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC----CCcceEeecHHHHHHHHHH
Confidence                                  47999999999999999999999986655555321    1245699999999988888


Q ss_pred             HHhC
Q psy15852        243 LKNP  246 (661)
Q Consensus       243 l~~~  246 (661)
                      |..+
T Consensus       265 m~~l  268 (284)
T KOG1457|consen  265 MNHL  268 (284)
T ss_pred             HHHh
Confidence            8764

>KOG0114|consensus

Probab=99.12  E-value=2.6e-10  Score=93.51  Aligned_cols=78  Identities=14%  Similarity=0.270  Sum_probs=71.2

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      .+-|||+|||+++|.+++.++|.+||.|..|+|-..+.|   +|.|||.|++..+|.+|+..+ +..+.++.+.|-+..+
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            367999999999999999999999999999999777665   999999999999999999998 6899999999998876


Q ss_pred             CC
Q psy15852        263 KP  264 (661)
Q Consensus       263 k~  264 (661)
                      ..
T Consensus        95 ~~   96 (124)
T KOG0114|consen   95 ED   96 (124)
T ss_pred             HH
Confidence            54

>KOG4207|consensus

Probab=99.12  E-value=8.8e-11  Score=108.19  Aligned_cols=77  Identities=27%  Similarity=0.480  Sum_probs=69.8

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      .|.|-+|..-++.++|+.+|++||.|-+|.|++|+.|+.++|||||.|....+|+.|    +..+++.+|+|+.|.|+.+
T Consensus        15 SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA----~damDG~~ldgRelrVq~a   90 (256)
T KOG4207|consen   15 SLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDA----LDAMDGAVLDGRELRVQMA   90 (256)
T ss_pred             eEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHH----HHhhcceeeccceeeehhh
Confidence            344455556999999999999999999999999999999999999999999999999    9999999999999988766


Q ss_pred             h
Q psy15852        181 K  181 (661)
Q Consensus       181 ~  181 (661)
                      .
T Consensus        91 r   91 (256)
T KOG4207|consen   91 R   91 (256)
T ss_pred             h
Confidence            4

>KOG4307|consensus

Probab=99.12  E-value=6.1e-09  Score=111.49  Aligned_cols=164  Identities=12%  Similarity=0.022  Sum_probs=106.3

Q ss_pred             eEEeeecccccCCcccceEEEEeCChHHHHHHHhCCCCcCCCcEEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy15852        445 IIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGY  524 (661)
Q Consensus       445 i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~~~~~~l~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~  524 (661)
                      |....|..++..+...|-++|.|....++++|+..+...+-.+.+.+.-+.....-..        .+...+-+.   + 
T Consensus       337 ~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P~g~~~~~~a--------~~~~~~~~~---~-  404 (944)
T KOG4307|consen  337 AQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGPPGNLGRNGA--------PPFQAGVPP---P-  404 (944)
T ss_pred             ccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceeecCCCccccccC--------ccccccCCC---C-
Confidence            5555566666666667999999999999999998888888888888865543321110        000000000   0 


Q ss_pred             CCCCCCCCCCCCCCCccccccccccCCCccccccccccCCCCCcccCCCccccccCCCCccccccccCCCeEEEcCCCCC
Q psy15852        525 GGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVD  604 (661)
Q Consensus       525 gg~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~  604 (661)
                             .+...                      .+...+.|-+......+          .-..-..+..|||..||+.
T Consensus       405 -------~~~~~----------------------hg~p~~~pr~~~~~gq~----------vp~P~~ag~~lyv~~lP~~  445 (944)
T KOG4307|consen  405 -------VIQNN----------------------HGRPIAPPRAMVRPGQN----------VPFPGGAGGALYVFQLPVM  445 (944)
T ss_pred             -------ccccc----------------------CCCCCCCcccccCCCCC----------CCCCCCccceEEeccCCcc
Confidence                   00000                      00000001000000000          0001234678999999999


Q ss_pred             CCHHHHHHHhhcCCCeeE-EEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcccC
Q psy15852        605 KITEELKEHFSKYGEIEN-VTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFYS  660 (661)
Q Consensus       605 ~te~dL~~~F~~~G~I~~-v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~~~  660 (661)
                      +++.++.++|+.--.|++ |.|-+.+ |++-++.|||.|..++++.+|....|.||+
T Consensus       446 t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~  501 (944)
T KOG4307|consen  446 TPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYP  501 (944)
T ss_pred             ccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhccccccc
Confidence            999999999998878877 5555554 699999999999999999999999999996

>KOG1457|consensus

Probab=99.11  E-value=1.2e-09  Score=101.86  Aligned_cols=82  Identities=20%  Similarity=0.350  Sum_probs=65.3

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccC-CCCCCcCcEEEEEeCCHHHHHHHHHhCC-Ccc---CCeEEEEE
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYD-KSKSQRKNFCFITFEHESVVIDLLKNPK-QKI---NDKEVDVK  258 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~-~~~g~~~g~afV~f~~~~~A~~Al~~~~-~~~---~g~~i~V~  258 (661)
                      .++|||.+||.++..-+|..+|..|---+.+.+... +..+..+-+|||.|.+..+|..|+.+++ ..|   .+..|+|.
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            489999999999999999999999876666665443 2224566899999999999999999974 444   45788998


Q ss_pred             eccCCCC
Q psy15852        259 KATPKPE  265 (661)
Q Consensus       259 ~a~~k~~  265 (661)
                      .|+....
T Consensus       114 lAKSNtK  120 (284)
T KOG1457|consen  114 LAKSNTK  120 (284)
T ss_pred             ehhcCcc
Confidence            8876553

>KOG1456|consensus

Probab=99.11  E-value=1.5e-08  Score=101.24  Aligned_cols=214  Identities=13%  Similarity=0.124  Sum_probs=150.9

Q ss_pred             ceEEeCCCCCCCCcHHHHHHHh-hhccccccccEEeecCCCCceeee------------ccccccc------cc-----c
Q psy15852         31 RKLFCPLSSYLELDYLQLWQYF-DWVSSSFSENCLLEDSIGKPLTVS------------CSHHYYL------FD-----Q   86 (661)
Q Consensus        31 r~lfVg~l~~~~te~~~l~~~F-~~g~~~~~~~~~~~d~~~~~~~~~------------~~~~~~l------~~-----~   86 (661)
                      .-|.|++|-..++| .||.+.- .+|  .+.-+..+.....-.+.+.            ......+      ++     .
T Consensus        32 pvvhvr~l~~~v~e-adl~eal~~fG--~i~yvt~~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NyStsq~  108 (494)
T KOG1456|consen   32 PVVHVRGLHQGVVE-ADLVEALSNFG--PIAYVTCMPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYSTSQC  108 (494)
T ss_pred             ceEEEeccccccch-hHHHHHHhcCC--ceEEEEeccccceeeeeeccccchhhheehhccCcccccCchhhcccchhhh
Confidence            45899999999999 9999999 999  6665555444222122222            2221111      11     0


Q ss_pred             cccceeeeeecCCCcEEE--EcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHH
Q psy15852         87 ILRTHFFYIMEAKNKMVS--HPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVI  163 (661)
Q Consensus        87 ~~r~~~~~~~~~~~~~~~--~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~  163 (661)
                      ..|.-  .+...-+++++  +-|+. .+|-+-|..+....|+|.+|.|++.  +|-   .|.|+|++.+.|++|    ..
T Consensus       109 i~R~g--~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~~AqrA----k~  177 (494)
T KOG1456|consen  109 IERPG--DESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVEVAQRA----KA  177 (494)
T ss_pred             hccCC--CCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechhHHHHHH----Hh
Confidence            01111  11112234433  33433 8999999999999999999999874  232   599999999999999    88


Q ss_pred             HhCCeeecc--eeehhhhhhccC---------------------------------------------------------
Q psy15852        164 AEGNHVINN--KKIEAKKAKAKS---------------------------------------------------------  184 (661)
Q Consensus       164 ~~~~~~i~g--~~i~v~~~~~~~---------------------------------------------------------  184 (661)
                      .+||..|..  -.++|.++++..                                                         
T Consensus       178 alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~  257 (494)
T KOG1456|consen  178 ALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDR  257 (494)
T ss_pred             hcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCccccc
Confidence            899877632  344444443321                                                         


Q ss_pred             ------------------------------CeeEecCCCcc-CCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEe
Q psy15852        185 ------------------------------GKIFVGGLSPE-MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF  233 (661)
Q Consensus       185 ------------------------------~~lfV~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f  233 (661)
                                                    +-+.|-+|... +.-+.|-.+|..||.|+.|++++.+     .|.|.|+.
T Consensus       258 ~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVem  332 (494)
T KOG1456|consen  258 HGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEM  332 (494)
T ss_pred             CCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEc
Confidence                                          45888889876 5667899999999999999999754     67899999


Q ss_pred             CCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        234 EHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       234 ~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      .+..+.++|+.-+ +..+-|.+|.|..++..
T Consensus       333 gd~~aver~v~hLnn~~lfG~kl~v~~SkQ~  363 (494)
T KOG1456|consen  333 GDAYAVERAVTHLNNIPLFGGKLNVCVSKQN  363 (494)
T ss_pred             CcHHHHHHHHHHhccCccccceEEEeecccc
Confidence            9999999999987 56788899999887643

>smart00362 RRM_2 RNA recognition motif

Probab=99.09  E-value=5.2e-10  Score=88.95  Aligned_cols=71  Identities=30%  Similarity=0.636  Sum_probs=65.1

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC-CccCCeEEEEE
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK-QKINDKEVDVK  258 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~-~~~~g~~i~V~  258 (661)
                      +|+|+|||..+++++|+++|.+||.|..+.+..+.  +.++++|||+|.+.++|.+|++.++ ..+.|+.|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999998876  6788999999999999999999874 88999998873

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.09  E-value=2.2e-10  Score=112.29  Aligned_cols=74  Identities=23%  Similarity=0.361  Sum_probs=65.1

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +++++.++++.+++++|+++|+.||+|.+|.|++++.   ++|||||+|.++++|+.|    + .+++..|.|+.|.|.+
T Consensus         5 rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~A----l-lLnG~~l~gr~V~Vt~   76 (260)
T PLN03120          5 RTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETA----L-LLSGATIVDQSVTITP   76 (260)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHH----H-HhcCCeeCCceEEEEe
Confidence            4555556666999999999999999999999998753   579999999999999997    5 5999999999999988


Q ss_pred             hh
Q psy15852        180 AK  181 (661)
Q Consensus       180 ~~  181 (661)
                      +.
T Consensus        77 a~   78 (260)
T PLN03120         77 AE   78 (260)
T ss_pred             cc
Confidence            75

>PLN03213 repressor of silencing 3; Provisional

Probab=99.09  E-value=2.4e-10  Score=117.50  Aligned_cols=75  Identities=19%  Similarity=0.376  Sum_probs=68.5

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCH--HHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE--SVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~--~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      .+|||+||++.++++||+.+|+.||.|.+|.|++  .+|  ||||||+|.+.  .++.+||..+ +..+.|+.|+|..|+
T Consensus        11 MRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213         11 VRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            5899999999999999999999999999999994  456  99999999987  6899999998 689999999999987


Q ss_pred             CC
Q psy15852        262 PK  263 (661)
Q Consensus       262 ~k  263 (661)
                      +.
T Consensus        87 P~   88 (759)
T PLN03213         87 EH   88 (759)
T ss_pred             HH
Confidence            64

>smart00360 RRM RNA recognition motif

Probab=99.08  E-value=3.1e-10  Score=89.90  Aligned_cols=59  Identities=44%  Similarity=0.580  Sum_probs=56.4

Q ss_pred             EcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        598 SHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       598 v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      |.|||..+++++|+++|++||.|..++++.++.+++++|+|||+|.+.++|.+|++.++
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~   59 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALN   59 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcC
Confidence            57899999999999999999999999999998889999999999999999999999876

>KOG0128|consensus

Probab=99.07  E-value=2.7e-11  Score=132.77  Aligned_cols=302  Identities=12%  Similarity=0.080  Sum_probs=203.0

Q ss_pred             cEEEEcCCC-cCCHHHHH-HHhhcCCCeeE-EEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852        101 KMVSHPGIV-HKITEELK-EHFSKYGEIEN-VTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus       101 ~~~~~~~~~-~~te~~L~-~~F~~~G~I~~-v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      +...+.|.+ ....-.|. .+|+.++-+.. .+...   ....+.+|+++-.++++|..+    ++.+.......-.+.+
T Consensus       480 ~~R~iWn~imty~~~~iag~Wle~~~lE~~~g~~~~---~R~~~R~ay~~~~~~~~~~ev----~~~~~r~Ere~gtl~~  552 (881)
T KOG0128|consen  480 KAREIWNFIMTYGGGSIAGKWLEAINLEREYGDGPS---ARKVLRKAYSQVVDPEDALEV----LEFFRRFEREYGTLES  552 (881)
T ss_pred             hhhHhhhccccCCcchHHHHHHHHHhHHHHhCCchh---HHHHHHHHHhcCcCchhHHHH----HHHHHHHHhccccHHH
Confidence            333344443 55666666 66665543211 22211   122556899999999999997    4444444333333322


Q ss_pred             hhh------------hccCCeeEecCCCccCCHH-HHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHH
Q psy15852        178 KKA------------KAKSGKIFVGGLSPEMKDE-EIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK  244 (661)
Q Consensus       178 ~~~------------~~~~~~lfV~nLp~~~te~-~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~  244 (661)
                      .-.            .-+.....+.++.+..... .++..|..+|.|+.|.++......+...++++.+..+.+++.|..
T Consensus       553 ~~~~~~~~~pr~~~~~~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~  632 (881)
T KOG0128|consen  553 FDLCPEKVLPRVYEAPLERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV  632 (881)
T ss_pred             HhhhHHhhcchhhhhhhhhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhccc
Confidence            221            1122456777887765554 678899999999999988633323333478888888888888876


Q ss_pred             hCCCccCCeEEEEEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCC
Q psy15852        245 NPKQKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLV  324 (661)
Q Consensus       245 ~~~~~~~g~~i~V~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  324 (661)
                      ..+..+.++.+.|..+.++...                                                          
T Consensus       633 pa~~~~a~~~~av~~ad~~~~~----------------------------------------------------------  654 (881)
T KOG0128|consen  633 PAGGALANRSAAVGLADAEEKE----------------------------------------------------------  654 (881)
T ss_pred             ccccccCCccccCCCCCchhhh----------------------------------------------------------
Confidence            6666666666555554443210                                                          


Q ss_pred             CCCCCCCCCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccc
Q psy15852        325 CRTGPMVQATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELE  404 (661)
Q Consensus       325 ~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~  404 (661)
                                      +                      .-..+.+++++..+             +++.++.+.+.+++
T Consensus       655 ----------------~----------------------~~kvs~n~~R~~~~-------------~fvsnl~~~~~~~d  683 (881)
T KOG0128|consen  655 ----------------E----------------------NFKVSPNEIRDLIK-------------IFVSNLSPKMSEED  683 (881)
T ss_pred             ----------------h----------------------ccCcCchHHHHHHH-------------HHHhhcchhhcCch
Confidence                            0                      00122244444332             34555666799999


Q ss_pred             hhhhhhccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHhCCCCcC
Q psy15852        405 IPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKI  484 (661)
Q Consensus       405 l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~~~~~~l  484 (661)
                      +...|..++                              .+..+++.--..+++.+|+|+|.|..++.+.+||.....++
T Consensus       684 l~~~~~~~~------------------------------~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~  733 (881)
T KOG0128|consen  684 LSERFSPSG------------------------------TIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCF  733 (881)
T ss_pred             hhhhcCccc------------------------------hhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhh
Confidence            999998884                              45555555455678899999999999999999994443221


Q ss_pred             CCcEEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCccccccccccCC
Q psy15852        485 NDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIG  564 (661)
Q Consensus       485 ~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  564 (661)
                      -|                                                                              
T Consensus       734 ~g------------------------------------------------------------------------------  735 (881)
T KOG0128|consen  734 FG------------------------------------------------------------------------------  735 (881)
T ss_pred             hh------------------------------------------------------------------------------
Confidence            11                                                                              


Q ss_pred             CCCcccCCCccccccCCCCccccccccCCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcC
Q psy15852        565 KPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKD  644 (661)
Q Consensus       565 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~  644 (661)
                                                  +.++||.|+||..|+++|+.+|+++|.+.+++++..+. |+++|.|||.|.+
T Consensus       736 ----------------------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~-gkpkg~a~v~y~~  786 (881)
T KOG0128|consen  736 ----------------------------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRA-GKPKGKARVDYNT  786 (881)
T ss_pred             ----------------------------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhc-cccccceeccCCC
Confidence                                        34689999999999999999999999999999998876 9999999999999


Q ss_pred             HHHHHHHHHhC
Q psy15852        645 TESLEKASVED  655 (661)
Q Consensus       645 ~e~A~~A~~~~  655 (661)
                      ..+|.++.++-
T Consensus       787 ea~~s~~~~s~  797 (881)
T KOG0128|consen  787 EADASRKVASV  797 (881)
T ss_pred             cchhhhhcccc
Confidence            99999988754

>KOG1365|consensus

Probab=99.06  E-value=9.5e-10  Score=110.08  Aligned_cols=153  Identities=18%  Similarity=0.226  Sum_probs=115.3

Q ss_pred             EcCCCcCCHHHHHHHhhcCC----CeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        105 HPGIVHKITEELKEHFSKYG----EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       105 ~~~~~~~te~~L~~~F~~~G----~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      .+|++++++.|+.++|..--    -.+.|-.+..++ |+..|-|||.|..+++|+.||     ..+...|.-|.|.+.++
T Consensus       167 RGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpd-grpTGdAFvlfa~ee~aq~aL-----~khrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  167 RGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPD-GRPTGDAFVLFACEEDAQFAL-----RKHRQNIGQRYIELFRS  240 (508)
T ss_pred             cCCCCCcchHHHHHhcCCCCcccCCccceEEEECCC-CCcccceEEEecCHHHHHHHH-----HHHHHHHhHHHHHHHHH
Confidence            46677999999999997432    345666666554 999999999999999999973     33334444444433222


Q ss_pred             h------------------------------------ccCCeeEecCCCccCCHHHHHHHHhcCC-CeEE--EEeccCCC
Q psy15852        181 K------------------------------------AKSGKIFVGGLSPEMKDEEIKAHFAQFG-NIIE--TEMPYDKS  221 (661)
Q Consensus       181 ~------------------------------------~~~~~lfV~nLp~~~te~~L~~~F~~~G-~i~~--v~i~~~~~  221 (661)
                      .                                    ....+|.+++||+..+.+||.++|..|. .|..  |+++.+..
T Consensus       241 TaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~q  320 (508)
T KOG1365|consen  241 TAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQ  320 (508)
T ss_pred             hHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCC
Confidence            1                                    1126899999999999999999999987 3443  67777654


Q ss_pred             CCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCC
Q psy15852        222 KSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKP  264 (661)
Q Consensus       222 ~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~  264 (661)
                       |+..|-|||+|.+.++|..|.... ++..+.|.|+|-.+...+
T Consensus       321 -GrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~ee  363 (508)
T KOG1365|consen  321 -GRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVEE  363 (508)
T ss_pred             -CCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHHH
Confidence             899999999999999999998876 455678999998876543

>smart00360 RRM RNA recognition motif

Probab=99.04  E-value=8.5e-10  Score=87.37  Aligned_cols=70  Identities=30%  Similarity=0.605  Sum_probs=64.6

Q ss_pred             ecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC-CccCCeEEEEE
Q psy15852        189 VGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK-QKINDKEVDVK  258 (661)
Q Consensus       189 V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~-~~~~g~~i~V~  258 (661)
                      |+|||..+++++|+++|++||.|..+.+..++.++.++++|||+|.+.++|.+|++.++ ..+.|+.|.|.
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            68999999999999999999999999999888788999999999999999999999884 78899988773

>KOG0130|consensus

Probab=99.04  E-value=1.7e-10  Score=99.07  Aligned_cols=76  Identities=21%  Similarity=0.433  Sum_probs=70.1

Q ss_pred             EEEEcCC-CcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        102 MVSHPGI-VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       102 ~~~~~~~-~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      +++|.+. +.++|++|.+.|..||+|..++|-.|..||-.||||+|+|.+.++|++|    +..+|+..|.+++|.|.|+
T Consensus        74 Ii~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A----~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   74 IIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAA----IDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             EEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHH----HHhccchhhhCCceeEEEE
Confidence            4555554 5999999999999999999999999999999999999999999999999    9999999999999999986


Q ss_pred             h
Q psy15852        181 K  181 (661)
Q Consensus       181 ~  181 (661)
                      -
T Consensus       150 F  150 (170)
T KOG0130|consen  150 F  150 (170)
T ss_pred             E
Confidence            3

>KOG0107|consensus

Probab=99.03  E-value=3.1e-10  Score=102.26  Aligned_cols=74  Identities=30%  Similarity=0.440  Sum_probs=66.8

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+.|||+||+ .+++.||+.+|..||+|.+|.|.+++     .|||||+|+++.||+.|    +..|++..|.|..|.|+
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DA----vr~LDG~~~cG~r~rVE   80 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDA----VRYLDGKDICGSRIRVE   80 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHH----HhhcCCccccCceEEEE
Confidence            5678888887 99999999999999999999999864     58999999999999999    99999999999999887


Q ss_pred             hhhc
Q psy15852        179 KAKA  182 (661)
Q Consensus       179 ~~~~  182 (661)
                      ...-
T Consensus        81 ~S~G   84 (195)
T KOG0107|consen   81 LSTG   84 (195)
T ss_pred             eecC
Confidence            6653

>KOG0116|consensus

Probab=99.02  E-value=1.7e-09  Score=114.24  Aligned_cols=81  Identities=25%  Similarity=0.442  Sum_probs=70.1

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKP  264 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k~  264 (661)
                      ..|||+|||.+++.++|+++|.+||.|+...|....-.++...||||+|.+.++++.||.+....++++++.|+...+..
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~~~  368 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRPGF  368 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEeccccc
Confidence            45999999999999999999999999999887764422444599999999999999999999889999999998876644


Q ss_pred             C
Q psy15852        265 E  265 (661)
Q Consensus       265 ~  265 (661)
                      .
T Consensus       369 ~  369 (419)
T KOG0116|consen  369 R  369 (419)
T ss_pred             c
Confidence            3

>KOG0111|consensus

Probab=99.01  E-value=3e-10  Score=105.45  Aligned_cols=84  Identities=24%  Similarity=0.519  Sum_probs=78.9

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC-CccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK-QKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~-~~~~g~~i~V~~a~  261 (661)
                      ..++|||++|..+++|.-|...|-+||.|.+|.++.|..+++.+|||||+|.-.|+|.+||..|+ ..|.||.|+|.+|.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            45799999999999999999999999999999999999999999999999999999999999985 79999999999999


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      |..-.
T Consensus        89 P~kik   93 (298)
T KOG0111|consen   89 PEKIK   93 (298)
T ss_pred             Ccccc
Confidence            87643

>KOG0129|consensus

Probab=99.00  E-value=4.8e-09  Score=109.83  Aligned_cols=161  Identities=19%  Similarity=0.350  Sum_probs=120.5

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCC-C--Cccc---EEEEEEeehhhHHHhhHHHHHHhCCe-ee-
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNT-G--RSRG---FAFIVFKDTESLEKASVEDVIAEGNH-VI-  170 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~t-g--~srG---~afV~F~~~e~A~~A~~~~~~~~~~~-~i-  170 (661)
                      .+++|+++++++++|++|...|..||.+ .|.++..... +  ..+|   |+|+.|+++.++.. |..++....+. .| 
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~-Ll~aC~~~~~~~yf~  336 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQS-LLSACSEGEGNYYFK  336 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHH-HHHHHhhcccceEEE
Confidence            4678889999999999999999999986 4566632211 1  2567   99999999999887 33324432222 22 


Q ss_pred             ------cceeehhhhhh--------------ccCCeeEecCCCccCCHHHHHHHHh-cCCCeEEEEeccCCCCCCcCcEE
Q psy15852        171 ------NNKKIEAKKAK--------------AKSGKIFVGGLSPEMKDEEIKAHFA-QFGNIIETEMPYDKSKSQRKNFC  229 (661)
Q Consensus       171 ------~g~~i~v~~~~--------------~~~~~lfV~nLp~~~te~~L~~~F~-~~G~i~~v~i~~~~~~g~~~g~a  229 (661)
                            ..+.+.|.+..              ...++|||++||..++.++|..+|. -||.|..+-|-.|++-+-++|-|
T Consensus       337 vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaG  416 (520)
T KOG0129|consen  337 VSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAG  416 (520)
T ss_pred             EecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcc
Confidence                  22333333321              2338999999999999999999999 59999999999998889999999


Q ss_pred             EEEeCCHHHHHHHHHhC----CCccCCeEEEEEecc
Q psy15852        230 FITFEHESVVIDLLKNP----KQKINDKEVDVKKAT  261 (661)
Q Consensus       230 fV~f~~~~~A~~Al~~~----~~~~~g~~i~V~~a~  261 (661)
                      =|+|.+..+-.+||.+-    .+.--.++|+|++-.
T Consensus       417 RVtFsnqqsYi~AIsarFvql~h~d~~KRVEIkPYv  452 (520)
T KOG0129|consen  417 RVTFSNQQAYIKAISARFVQLDHTDIDKRVEIKPYV  452 (520)
T ss_pred             eeeecccHHHHHHHhhheEEEeccccceeeeeccee
Confidence            99999999999999884    232233578887655

>smart00361 RRM_1 RNA recognition motif

Probab=99.00  E-value=9.4e-10  Score=87.84  Aligned_cols=61  Identities=21%  Similarity=0.499  Sum_probs=55.4

Q ss_pred             HHHHHHHhh----cCCCeeEEE-EeeCCCC--CCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852        113 TEELKEHFS----KYGEIENVT-LKSDPNT--GRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus       113 e~~L~~~F~----~~G~I~~v~-l~~~~~t--g~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      +++|+++|+    +||.|.+|. |+.++.+  ++++|||||+|.+.++|.+|    +..+|+..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A----~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARA----IVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHH----HHHhCCCEECCEEEEe
Confidence            678999999    999999995 7777766  89999999999999999999    9999999999999865

>KOG0106|consensus

Probab=99.00  E-value=7.8e-10  Score=105.65  Aligned_cols=72  Identities=19%  Similarity=0.451  Sum_probs=63.5

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      .++||++||+.+.+.+|+.+|..||.|.+|.+.        .||+||+|.+..+|..|+..+ +..|.+..+.|.++...
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 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            368999999999999999999999999999874        688999999999999999887 57888888888888754


Q ss_pred             C
Q psy15852        264 P  264 (661)
Q Consensus       264 ~  264 (661)
                      .
T Consensus        74 ~   74 (216)
T KOG0106|consen   74 R   74 (216)
T ss_pred             c
Confidence            3

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.99  E-value=1.1e-09  Score=105.68  Aligned_cols=73  Identities=21%  Similarity=0.283  Sum_probs=63.3

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      ++++.++.+.+|+++|+++|+.||+|.+|+|+++   +..+|||||+|.++++|+.|     +.|++..|.+++|.|.++
T Consensus         7 TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D---~et~gfAfVtF~d~~aaetA-----llLnGa~l~d~~I~It~~   78 (243)
T PLN03121          7 TAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS---GEYACTAYVTFKDAYALETA-----VLLSGATIVDQRVCITRW   78 (243)
T ss_pred             EEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC---CCcceEEEEEECCHHHHHHH-----HhcCCCeeCCceEEEEeC
Confidence            4555555569999999999999999999999998   45668999999999999995     689999999999988765


Q ss_pred             h
Q psy15852        181 K  181 (661)
Q Consensus       181 ~  181 (661)
                      .
T Consensus        79 ~   79 (243)
T PLN03121         79 G   79 (243)
T ss_pred             c
Confidence            4

>smart00362 RRM_2 RNA recognition motif

Probab=98.99  E-value=2e-09  Score=85.48  Aligned_cols=70  Identities=34%  Similarity=0.542  Sum_probs=62.3

Q ss_pred             EEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852        102 MVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus       102 ~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      +++.++++.+++++|+++|++||+|..+.+..++  +.++|+|||+|.+.++|++|    +..+++..+.|+++.|
T Consensus         2 v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a----~~~~~~~~~~~~~i~v   71 (72)
T smart00362        2 LFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKA----IEALNGTKLGGRPLRV   71 (72)
T ss_pred             EEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHH----HHHhCCcEECCEEEee
Confidence            4555555699999999999999999999999876  78899999999999999999    8889999999988875

>PLN03213 repressor of silencing 3; Provisional

Probab=98.96  E-value=1.2e-09  Score=112.43  Aligned_cols=75  Identities=24%  Similarity=0.299  Sum_probs=65.2

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeeh--hhHHHhhHHHHHHhCCeeecceeehh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDT--ESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~--e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      -+++|++|.+++++++|+.+|+.||.|.+|.|++  .||  ||||||+|.+.  .++.+|    +..||+..+.|+.|+|
T Consensus        11 MRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKA----ISaLNGAEWKGR~LKV   82 (759)
T PLN03213         11 VRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKL----FSTYNGCVWKGGRLRL   82 (759)
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHH----HHHhcCCeecCceeEE
Confidence            3455555556999999999999999999999995  456  99999999998  678888    9999999999999999


Q ss_pred             hhhhc
Q psy15852        178 KKAKA  182 (661)
Q Consensus       178 ~~~~~  182 (661)
                      ..+++
T Consensus        83 NKAKP   87 (759)
T PLN03213         83 EKAKE   87 (759)
T ss_pred             eeccH
Confidence            88764

>KOG0111|consensus

Probab=98.95  E-value=3.6e-10  Score=104.94  Aligned_cols=83  Identities=19%  Similarity=0.399  Sum_probs=75.7

Q ss_pred             CCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852         98 AKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus        98 ~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ...+++||+.+. +++|.-|...|-.||.|.+|.++.|-.++++||||||+|...|||.+|    +..+|..+|.||.|.
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaA----iDNMnesEL~Grtir   83 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAA----IDNMNESELFGRTIR   83 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHH----hhcCchhhhcceeEE
Confidence            345566666665 999999999999999999999999999999999999999999999999    999999999999999


Q ss_pred             hhhhhccC
Q psy15852        177 AKKAKAKS  184 (661)
Q Consensus       177 v~~~~~~~  184 (661)
                      |..++|..
T Consensus        84 VN~AkP~k   91 (298)
T KOG0111|consen   84 VNLAKPEK   91 (298)
T ss_pred             EeecCCcc
Confidence            99998754

>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=98.94  E-value=5.2e-09  Score=83.58  Aligned_cols=73  Identities=26%  Similarity=0.581  Sum_probs=65.9

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC-CccCCeEEEEEe
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK-QKINDKEVDVKK  259 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~-~~~~g~~i~V~~  259 (661)
                      +|+|+|||..+++++|+++|+.||.|..+.+..++.+ ..+++|||+|.+.++|..|++.+. ..++|+.+.|.+
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            4899999999999999999999999999999987654 678999999999999999999984 559999998864

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).

>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=98.93  E-value=4e-09  Score=84.25  Aligned_cols=63  Identities=37%  Similarity=0.492  Sum_probs=58.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        595 KMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       595 ~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      +|+|.+||+.+++++|+++|..||.|..+++..++.+ .++|+|||+|.+.++|..|+..++..
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~   63 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGK   63 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCC
Confidence            4899999999999999999999999999999998774 88999999999999999999987654

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).

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.90  E-value=4.3e-09  Score=107.68  Aligned_cols=79  Identities=23%  Similarity=0.563  Sum_probs=75.4

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC-CccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK-QKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~-~~~~g~~i~V~~a~~  262 (661)
                      .++|||+|||..+++++|+++|.+||.|..+.+..++.++.++|||||+|.+.++|..|+..++ ..|.|++|.|.++..
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            5899999999999999999999999999999999998889999999999999999999999985 899999999999764

>KOG0108|consensus

Probab=98.90  E-value=3.2e-09  Score=112.88  Aligned_cols=81  Identities=22%  Similarity=0.455  Sum_probs=77.4

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      +.|||+|+|+++++++|.++|+..|.|.+++++.|+.||+++||||++|.+.++|.+|++.+ +.++.|++|+|.|+...
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            78999999999999999999999999999999999999999999999999999999999998 58999999999998876


Q ss_pred             CC
Q psy15852        264 PE  265 (661)
Q Consensus       264 ~~  265 (661)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            54

>PF13893 RRM_5: RNA recognition motif

Probab=98.89  E-value=3.2e-09  Score=80.76  Aligned_cols=56  Identities=30%  Similarity=0.548  Sum_probs=50.2

Q ss_pred             HHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        116 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       116 L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      |+++|++||+|.+|.+..++     +++|||+|.+.++|++|    +..+|+..+.|++|.|.++
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-----RGFAFVEFASVEDAQKA----IEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHH----HHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHH----HHHhCCCEECCcEEEEEEC
Confidence            78999999999999998753     68999999999999999    8999999999999998764

(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 ....

>KOG0415|consensus

Probab=98.84  E-value=3.1e-09  Score=105.39  Aligned_cols=85  Identities=26%  Similarity=0.378  Sum_probs=79.1

Q ss_pred             eeecCCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecce
Q psy15852         94 YIMEAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK  173 (661)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~  173 (661)
                      ...++.+-+|+.+|.|-+++++|.-+|+.||+|.+|.|++|..||-+.-||||+|.+.+++++|    .-.+++..|..+
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~A----yFKMdNvLIDDr  309 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQA----YFKMDNVLIDDR  309 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHH----Hhhhcceeeccc
Confidence            3556778899999999999999999999999999999999999999999999999999999999    899999999999


Q ss_pred             eehhhhhhc
Q psy15852        174 KIEAKKAKA  182 (661)
Q Consensus       174 ~i~v~~~~~  182 (661)
                      .|.|.++..
T Consensus       310 RIHVDFSQS  318 (479)
T KOG0415|consen  310 RIHVDFSQS  318 (479)
T ss_pred             eEEeehhhh
Confidence            999987764

>KOG0108|consensus

Probab=98.83  E-value=4.6e-09  Score=111.63  Aligned_cols=80  Identities=25%  Similarity=0.352  Sum_probs=72.6

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      ..++|++.+++++|++|.++|++.|+|.+++++.|+.||++|||||++|.+.++|..|    +..+|+..+.|++|+|.+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a----~~~lNg~~~~gr~l~v~~   94 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERA----IRNLNGAEFNGRKLRVNY   94 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHH----HHhcCCcccCCceEEeec
Confidence            4455555555999999999999999999999999999999999999999999999999    999999999999999998


Q ss_pred             hhcc
Q psy15852        180 AKAK  183 (661)
Q Consensus       180 ~~~~  183 (661)
                      +...
T Consensus        95 ~~~~   98 (435)
T KOG0108|consen   95 ASNR   98 (435)
T ss_pred             cccc
Confidence            7643

>smart00361 RRM_1 RNA recognition motif

Probab=98.83  E-value=1.2e-08  Score=81.43  Aligned_cols=60  Identities=18%  Similarity=0.380  Sum_probs=53.1

Q ss_pred             HHHHHHHHh----cCCCeEEEE-eccCCCC--CCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEE
Q psy15852        198 DEEIKAHFA----QFGNIIETE-MPYDKSK--SQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDV  257 (661)
Q Consensus       198 e~~L~~~F~----~~G~i~~v~-i~~~~~~--g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V  257 (661)
                      +++|+++|+    +||.|.+|. ++.++.+  +.++|||||+|.+.++|.+|++.+ +..+.|+.|.+
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            578888888    999999995 6666666  889999999999999999999987 68999999876

>KOG0128|consensus

Probab=98.80  E-value=1.1e-09  Score=120.52  Aligned_cols=146  Identities=20%  Similarity=0.233  Sum_probs=121.0

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      +.|+..+++.+.+++|...|..+|.+..+++...+++++.||+|||+|..+++|.+|    +.....+.+.         
T Consensus       669 ~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aa----V~f~d~~~~g---------  735 (881)
T KOG0128|consen  669 KIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAA----VAFRDSCFFG---------  735 (881)
T ss_pred             HHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhh----hhhhhhhhhh---------
Confidence            355666667999999999999999998888887778899999999999999999997    5444444333         


Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                         ...++|+|+|+..|.++|+.+++++|.+.+..++..+. |+++|.|+|.|.++.++.+++... ...+.-+.+.|..
T Consensus       736 ---K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~-gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~v  811 (881)
T KOG0128|consen  736 ---KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRA-GKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQV  811 (881)
T ss_pred             ---hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhc-cccccceeccCCCcchhhhhcccchhhhhhhcCccccc
Confidence               34699999999999999999999999999998887665 999999999999999999998886 3455556666666


Q ss_pred             ccCC
Q psy15852        260 ATPK  263 (661)
Q Consensus       260 a~~k  263 (661)
                      ..+.
T Consensus       812 snp~  815 (881)
T KOG0128|consen  812 SNPE  815 (881)
T ss_pred             cCCc
Confidence            5553

>KOG4210|consensus

Probab=98.79  E-value=6.7e-09  Score=105.57  Aligned_cols=163  Identities=20%  Similarity=0.298  Sum_probs=127.0

Q ss_pred             CcEEEEcCC-CcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGI-VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~-~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+.++++.. ..+.+.++..++..+|.+..+.+........++|++++.|...+.+..|    +.......+.+..+...
T Consensus        88 ~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~----l~~s~~~~~~~~~~~~d  163 (285)
T KOG4210|consen   88 SSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAA----LEESGSKVLDGNKGEKD  163 (285)
T ss_pred             cccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHH----HHhhhccccccccccCc
Confidence            344444444 4777777899999999988888887777788999999999999999997    33222233333333221


Q ss_pred             hhh---------------ccCCeeE-ecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHH
Q psy15852        179 KAK---------------AKSGKIF-VGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDL  242 (661)
Q Consensus       179 ~~~---------------~~~~~lf-V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A  242 (661)
                      ...               ....++| |.+|++.+++++|+.+|..+|.|..++++.++.++.++|||+|.|.....+.++
T Consensus       164 l~~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~  243 (285)
T KOG4210|consen  164 LNTRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLA  243 (285)
T ss_pred             ccccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHH
Confidence            110               1124555 999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhCCCccCCeEEEEEeccCCCCC
Q psy15852        243 LKNPKQKINDKEVDVKKATPKPEP  266 (661)
Q Consensus       243 l~~~~~~~~g~~i~V~~a~~k~~~  266 (661)
                      +......+.++++.+....+....
T Consensus       244 ~~~~~~~~~~~~~~~~~~~~~~~~  267 (285)
T KOG4210|consen  244 LNDQTRSIGGRPLRLEEDEPRPKS  267 (285)
T ss_pred             hhcccCcccCcccccccCCCCccc
Confidence            887557889999999988876543

>PF13893 RRM_5: RNA recognition motif

Probab=98.78  E-value=2.5e-08  Score=75.83  Aligned_cols=55  Identities=18%  Similarity=0.385  Sum_probs=48.6

Q ss_pred             HHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        201 IKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       201 L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      |.++|++||+|..+.+..+.     +++|||+|.+.++|.+|++.+ +..+.|++|+|.|+
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            68899999999999997653     699999999999999999976 68899999999985

(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 ....

>KOG4208|consensus

Probab=98.69  E-value=2.8e-08  Score=92.40  Aligned_cols=69  Identities=20%  Similarity=0.358  Sum_probs=61.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcC-CCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh-CCcccC
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKY-GEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE-DVYFYS  660 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~-G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~-~~~~~~  660 (661)
                      ...-++|.++|+-+.+.+|..+|.+| |.|..+++-|++.||.|+|||||+|++++.|+.|-+. ++||++
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~  118 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLM  118 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhh
Confidence            34568999999999999999999999 7888899989999999999999999999999999885 555543

>KOG0415|consensus

Probab=98.68  E-value=2e-08  Score=99.79  Aligned_cols=84  Identities=24%  Similarity=0.434  Sum_probs=78.2

Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                      .|+.+-|||.-|.+-++++||+-+|+.||+|.+|.+++|..||.+-.||||+|++.+++++|.=+| +..|+.++|+|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            466789999999999999999999999999999999999999999999999999999999998777 7899999999998


Q ss_pred             ccCCC
Q psy15852        260 ATPKP  264 (661)
Q Consensus       260 a~~k~  264 (661)
                      +++-.
T Consensus       316 SQSVs  320 (479)
T KOG0415|consen  316 SQSVS  320 (479)
T ss_pred             hhhhh
Confidence            87654

>KOG4208|consensus

Probab=98.67  E-value=2.9e-08  Score=92.32  Aligned_cols=79  Identities=22%  Similarity=0.349  Sum_probs=69.1

Q ss_pred             cCCCcEEEEcCCC-cCCHHHHHHHhhcC-CCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeeccee
Q psy15852         97 EAKNKMVSHPGIV-HKITEELKEHFSKY-GEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK  174 (661)
Q Consensus        97 ~~~~~~~~~~~~~-~~te~~L~~~F~~~-G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~  174 (661)
                      .....++|+.-+| -+.+.+|..+|.+| |.|+.+++-+++.||.|||||||+|++++.|+-|    +..+|+..+.++-
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~Ia----AETMNNYLl~e~l  121 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIA----AETMNNYLLMEHL  121 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHH----HHHhhhhhhhhhe
Confidence            3445677777777 88999999999999 7899999999999999999999999999999999    9999999998877


Q ss_pred             ehhhh
Q psy15852        175 IEAKK  179 (661)
Q Consensus       175 i~v~~  179 (661)
                      +.+..
T Consensus       122 L~c~v  126 (214)
T KOG4208|consen  122 LECHV  126 (214)
T ss_pred             eeeEE
Confidence            66543

>KOG4660|consensus

Probab=98.66  E-value=5.3e-07  Score=95.59  Aligned_cols=147  Identities=18%  Similarity=0.201  Sum_probs=102.1

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      +++++++.++++++++++|..+|+.||+|.+|+.-+     ..+|.+||+|.+..+|++|    +.+++...+.|+.|+.
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~-----~~~~~~~v~FyDvR~A~~A----lk~l~~~~~~~~~~k~  144 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP-----NKRGIVFVEFYDVRDAERA----LKALNRREIAGKRIKR  144 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc-----ccCceEEEEEeehHhHHHH----HHHHHHHHhhhhhhcC
Confidence            456788888888999999999999999999975544     4578999999999999999    9999999999988873


Q ss_pred             hhhhccC---------------------------CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEE
Q psy15852        178 KKAKAKS---------------------------GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCF  230 (661)
Q Consensus       178 ~~~~~~~---------------------------~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~af  230 (661)
                      .......                           -.+|+- |++..+..-++..++-+|.+.. +.     ++.-...-|
T Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P~~s~~~~~~~~~~~~~~~~-~~-----~~~~~hq~~  217 (549)
T KOG4660|consen  145 PGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LSPTRSSILLEHISSVDGSSPG-RE-----TPLLNHQRF  217 (549)
T ss_pred             CCcccccchhcccchhhhhccchhhcCCCCCCcCCcceee-eccchhhhhhhcchhccCcccc-cc-----ccchhhhhh
Confidence            2211100                           234433 7777777666667777776654 22     122223467


Q ss_pred             EEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        231 ITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       231 V~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      +.|.+..++..++..++..+.+....+.+.
T Consensus       218 ~~~~~~~s~a~~~~~~G~~~s~~~~v~t~S  247 (549)
T KOG4660|consen  218 VEFADNRSYAFSEPRGGFLISNSSGVITFS  247 (549)
T ss_pred             hhhccccchhhcccCCceecCCCCceEEec
Confidence            778777777555544445555555444443

>KOG4454|consensus

Probab=98.66  E-value=5.8e-09  Score=97.24  Aligned_cols=131  Identities=21%  Similarity=0.341  Sum_probs=111.5

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+++++.|+. .++|+-|.++|-+-|+|..|.|+.+++ ++.| ||||.|.++-+...|    +..+|+..+.++++.+.
T Consensus         9 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    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLA----GQLENGDDLEEDEEQRT   82 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhh----hhhcccchhccchhhcc
Confidence            3455566665 999999999999999999999999876 6777 999999999999999    89999999999888774


Q ss_pred             hhhccCCeeEecC----CCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHh
Q psy15852        179 KAKAKSGKIFVGG----LSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN  245 (661)
Q Consensus       179 ~~~~~~~~lfV~n----Lp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~  245 (661)
                              ++.++    |...++++.+...|+.-+++..+++..+.+ ++++.+.|+.+...-+.-.++..
T Consensus        83 --------~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d-~rnrn~~~~~~qr~~~~P~~~~~  144 (267)
T KOG4454|consen   83 --------LRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDND-GRNRNFGFVTYQRLCAVPFALDL  144 (267)
T ss_pred             --------cccCCCcchhhhhcchhhheeeecccCCCCCcccccccc-CCccCccchhhhhhhcCcHHhhh
Confidence                    55566    778899999999999999999999999877 88899999988766555555544

>KOG0153|consensus

Probab=98.57  E-value=1.6e-07  Score=93.64  Aligned_cols=73  Identities=27%  Similarity=0.506  Sum_probs=66.7

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC--CCccCCeEEEEEeccC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP--KQKINDKEVDVKKATP  262 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~--~~~~~g~~i~V~~a~~  262 (661)
                      .+|||++|-..+++.+|+++|.+||+|+++.+...      +++|||+|.+.++|++|.++.  ...|+|++|.|.|..+
T Consensus       229 ~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  229 KTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             eEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            78999999999999999999999999999999754      679999999999999999886  3678999999999887


Q ss_pred             C
Q psy15852        263 K  263 (661)
Q Consensus       263 k  263 (661)
                      +
T Consensus       303 ~  303 (377)
T KOG0153|consen  303 K  303 (377)
T ss_pred             c
Confidence            3

>KOG1548|consensus

Probab=98.54  E-value=1e-06  Score=87.95  Aligned_cols=194  Identities=14%  Similarity=0.080  Sum_probs=120.0

Q ss_pred             cccc-ccccCCCCCcCccchhhhhhccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEE
Q psy15852        387 VADN-LLLCDNFPSIRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFI  465 (661)
Q Consensus       387 ~~~~-~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV  465 (661)
                      ..+. ++|.++.+++|.+++.++|+.++.+....+++                      --.|++-++.. |+.+|-|.+
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~----------------------epk~KlYrd~~-G~lKGDaLc  188 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTG----------------------EPKVKLYRDNQ-GKLKGDALC  188 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCC----------------------CeeEEEEecCC-CCccCceEE
Confidence            3444 45554444599999999999986432211111                      13456666655 899999999


Q ss_pred             EeCChHHHHHHHhCC-CCcCCCcEEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccc
Q psy15852        466 TFEHESVVIDLLKNP-KQKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLWQ  544 (661)
Q Consensus       466 ~F~~~e~A~~Ai~~~-~~~l~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~~~~~~~~~~~~  544 (661)
                      +|-..+++.-|+..+ ...+.|+.|.|..|.-.....-                                     ..   
T Consensus       189 ~y~K~ESVeLA~~ilDe~~~rg~~~rVerAkfq~Kge~-------------------------------------~~---  228 (382)
T KOG1548|consen  189 CYIKRESVELAIKILDEDELRGKKLRVERAKFQMKGEY-------------------------------------DA---  228 (382)
T ss_pred             EeecccHHHHHHHHhCcccccCcEEEEehhhhhhccCc-------------------------------------Cc---
Confidence            999999999999544 4778999999998874421100                                     00   


Q ss_pred             cccccCCCccccccccccCCCCCcccCCCccccccCCCCccccccccCCCeEEEcCCCC----CCC-------HHHHHHH
Q psy15852        545 FFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIV----DKI-------TEELKEH  613 (661)
Q Consensus       545 ~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~----~~t-------e~dL~~~  613 (661)
                               +   ........+.-.-.....+.++........+.....++|+++|+-.    +.+       ++||++-
T Consensus       229 ---------~---~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~ee  296 (382)
T KOG1548|consen  229 ---------S---KKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEE  296 (382)
T ss_pred             ---------c---cccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHH
Confidence                     0   0000000000000001111111111111122234467888888854    444       4678888


Q ss_pred             hhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCccc
Q psy15852        614 FSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY  659 (661)
Q Consensus       614 F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~~  659 (661)
                      |.+||+|.+|.|.-.+    +.|.+-|.|.|.++|..+|.-++.=|
T Consensus       297 c~K~G~v~~vvv~d~h----PdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  297 CEKFGQVRKVVVYDRH----PDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             HHHhCCcceEEEeccC----CCceeEEEeCChHHHHHHHHHhcCee
Confidence            9999999999888544    58889999999999999999876533

>KOG0226|consensus

Probab=98.53  E-value=4e-08  Score=93.89  Aligned_cols=143  Identities=20%  Similarity=0.338  Sum_probs=116.8

Q ss_pred             HHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh-----------hccCC
Q psy15852        117 KEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA-----------KAKSG  185 (661)
Q Consensus       117 ~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~-----------~~~~~  185 (661)
                      ...|+.|-.+...+++++.. +.-++++|+.|.....-.++    ....+++.+.-.+++....           ...+.
T Consensus       117 ~~~f~~~p~L~ktk~v~~~p-~~~~~~~~~~~k~s~a~~k~----~~~~~~Kki~~~~VR~a~gtswedPsl~ew~~~Df  191 (290)
T KOG0226|consen  117 PVVFSEYPSLVKTKLVRDRP-QPIRPEAFESFKASDALLKA----ETEKEKKKIGKPPVRLAAGTSWEDPSLAEWDEDDF  191 (290)
T ss_pred             hhhhccchhhhhhhhhhcCC-CccCcccccCcchhhhhhhh----ccccccccccCcceeeccccccCCcccccCccccc
Confidence            67788887777777887654 77889999999887777776    5555666665554443222           12347


Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCC
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKP  264 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~  264 (661)
                      +||.+.|..+++++.|...|.+|-.-...++++++.|++++||+||.|.+.+++..|++.+ +.+++.++|.++....+.
T Consensus       192 RIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  192 RIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             eeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHHh
Confidence            9999999999999999999999998888999999999999999999999999999999998 688999999988766654

>KOG0132|consensus

Probab=98.51  E-value=1.9e-07  Score=101.83  Aligned_cols=75  Identities=20%  Similarity=0.372  Sum_probs=69.5

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ++|||+.|+..+++.||..+|+.||+|.+|.++.      ++++|||+.....+|.+|+.++ +..+.++.|+|.|+..+
T Consensus       422 rTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  422 RTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            7999999999999999999999999999999854      4899999999999999999998 68999999999999876


Q ss_pred             CC
Q psy15852        264 PE  265 (661)
Q Consensus       264 ~~  265 (661)
                      .-
T Consensus       496 G~  497 (894)
T KOG0132|consen  496 GP  497 (894)
T ss_pred             Cc
Confidence            43

>KOG0112|consensus

Probab=98.44  E-value=1.2e-07  Score=104.99  Aligned_cols=157  Identities=17%  Similarity=0.293  Sum_probs=129.0

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      .+++++..++...+++.+|+..|..+|.|.+|.|..-+. ++---|+||.|.+-..+-.|    ...+.+..|..-.+.+
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~a----k~e~s~~~I~~g~~r~  445 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSA----KFEESGPLIGNGTHRI  445 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCccc----chhhcCCccccCcccc
Confidence            356677777777999999999999999999999987533 55555999999999999999    8888888886666666


Q ss_pred             hhhhc---cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC-
Q psy15852        178 KKAKA---KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND-  252 (661)
Q Consensus       178 ~~~~~---~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g-  252 (661)
                      ....+   ..+.+++++|+.++....|...|..||.|..|.+      .+..-||+|.|++...|+.|+..+ +..|.+ 
T Consensus       446 glG~~kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy------~hgq~yayi~yes~~~aq~a~~~~rgap~G~P  519 (975)
T KOG0112|consen  446 GLGQPKSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY------RHGQPYAYIQYESPPAAQAATHDMRGAPLGGP  519 (975)
T ss_pred             cccccccccceeeccCCCCCCChHHHHHHHhhccCcceeeec------ccCCcceeeecccCccchhhHHHHhcCcCCCC
Confidence            55532   3478999999999999999999999999999888      334679999999999999999887 566655 


Q ss_pred             -eEEEEEeccCCCC
Q psy15852        253 -KEVDVKKATPKPE  265 (661)
Q Consensus       253 -~~i~V~~a~~k~~  265 (661)
                       +.+.|.++.+...
T Consensus       520 ~~r~rvdla~~~~~  533 (975)
T KOG0112|consen  520 PRRLRVDLASPPGA  533 (975)
T ss_pred             CcccccccccCCCC
Confidence             6788888876543

>KOG0226|consensus

Probab=98.38  E-value=9.1e-07  Score=84.74  Aligned_cols=68  Identities=21%  Similarity=0.316  Sum_probs=65.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcccC
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFYS  660 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~~~  660 (661)
                      .-+||++.|-.+++++-|...|.+|-.....++++|+.||+++|||||.|.+++|+..|+.+++.-|-
T Consensus       190 DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyV  257 (290)
T KOG0226|consen  190 DFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYV  257 (290)
T ss_pred             cceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhccccc
Confidence            46899999999999999999999999999999999999999999999999999999999999988774

>KOG0132|consensus

Probab=98.25  E-value=1.2e-06  Score=95.82  Aligned_cols=97  Identities=23%  Similarity=0.256  Sum_probs=76.6

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +||++.++...++|.||..+|+.||+|.+|.++.      +||||||.+....+|.+|    +.+++...+..+.|++.|
T Consensus       422 rTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~ka----lqkl~n~kv~~k~Iki~W  491 (894)
T KOG0132|consen  422 RTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKA----LQKLSNVKVADKTIKIAW  491 (894)
T ss_pred             eeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHH----HHHHhcccccceeeEEee
Confidence            4556666666999999999999999999999986      478999999999999999    889999999999999999


Q ss_pred             hhccC----------CeeEecCCCccCCHHHHHHHHh
Q psy15852        180 AKAKS----------GKIFVGGLSPEMKDEEIKAHFA  206 (661)
Q Consensus       180 ~~~~~----------~~lfV~nLp~~~te~~L~~~F~  206 (661)
                      +..+-          -.+=|.-||+..-..+|+.++.
T Consensus       492 a~g~G~kse~k~~wD~~lGVt~IP~~kLt~dl~~~~e  528 (894)
T KOG0132|consen  492 AVGKGPKSEYKDYWDVELGVTYIPWEKLTDDLEAWCE  528 (894)
T ss_pred             eccCCcchhhhhhhhcccCeeEeehHhcCHHHHHhhh
Confidence            86432          1234555677644444655553

>KOG0153|consensus

Probab=98.23  E-value=1.6e-06  Score=86.80  Aligned_cols=75  Identities=27%  Similarity=0.465  Sum_probs=62.8

Q ss_pred             CCcEEEEcCC-CcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         99 KNKMVSHPGI-VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        99 ~~~~~~~~~~-~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      .-+++|++++ +.++|.+|+++|.+||+|.++.+...+      ++|||+|.+.++|++|+   ...++...|.|++|.|
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aa---e~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAA---EKSFNKLVINGFRLKI  297 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHH---HhhcceeeecceEEEE
Confidence            3455555555 699999999999999999999998753      49999999999999982   3346788899999999


Q ss_pred             hhhhc
Q psy15852        178 KKAKA  182 (661)
Q Consensus       178 ~~~~~  182 (661)
                      .|..+
T Consensus       298 ~Wg~~  302 (377)
T KOG0153|consen  298 KWGRP  302 (377)
T ss_pred             EeCCC
Confidence            99887

>KOG4661|consensus

Probab=98.22  E-value=2.4e-06  Score=89.89  Aligned_cols=80  Identities=16%  Similarity=0.453  Sum_probs=73.2

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ++|||.+|...+...||+.+|++||+|.-.+++.+..+.-.+.|+||++.+.++|.+||..+ ...|.|+.|.|..++..
T Consensus       406 RNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKNE  485 (940)
T KOG4661|consen  406 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKNE  485 (940)
T ss_pred             cceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecccC
Confidence            68999999999999999999999999999999988777667999999999999999999998 57899999999988754


Q ss_pred             C
Q psy15852        264 P  264 (661)
Q Consensus       264 ~  264 (661)
                      +
T Consensus       486 p  486 (940)
T KOG4661|consen  486 P  486 (940)
T ss_pred             c
Confidence            4

>KOG0533|consensus

Probab=98.19  E-value=2.7e-06  Score=83.53  Aligned_cols=64  Identities=28%  Similarity=0.351  Sum_probs=60.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      ..+|+|.|||+.++++||++||..||.+..|-|..|+. |++.|.|-|.|...+||++|+++.+.
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~-G~s~Gta~v~~~r~~DA~~avk~~~g  146 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRA-GRSLGTADVSFNRRDDAERAVKKYNG  146 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCC-CCCCccceeeecchHhHHHHHHHhcC
Confidence            47899999999999999999999999999999999986 99999999999999999999998775

>KOG4660|consensus

Probab=98.16  E-value=7.9e-05  Score=79.47  Aligned_cols=68  Identities=19%  Similarity=0.364  Sum_probs=60.4

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEE
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVD  256 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~  256 (661)
                      .++|+|-|||..+++++|+.+|+.||+|+.|+.-     -..+|..||+|.+.-+|+.|++++ ...+.|+.|.
T Consensus        75 ~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t-----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   75 QGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET-----PNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc-----cccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            4789999999999999999999999999996553     445899999999999999999998 4678888877

>KOG0116|consensus

Probab=98.16  E-value=7.6e-06  Score=86.84  Aligned_cols=78  Identities=18%  Similarity=0.298  Sum_probs=62.4

Q ss_pred             ccccCCCCCcCccchhhhhhccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCCh
Q psy15852        391 LLLCDNFPSIRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHE  470 (661)
Q Consensus       391 ~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~  470 (661)
                      +++.++.+++++.+|.++|..|                              |+|....|....-.++..+||||+|.+.
T Consensus       291 i~V~nlP~da~~~~l~~~Fk~F------------------------------G~Ik~~~I~vr~~~~~~~~fgFV~f~~~  340 (419)
T KOG0116|consen  291 IFVKNLPPDATPAELEEVFKQF------------------------------GPIKEGGIQVRSPGGKNPCFGFVEFENA  340 (419)
T ss_pred             eEeecCCCCCCHHHHHHHHhhc------------------------------ccccccceEEeccCCCcCceEEEEEeec
Confidence            4555555559999999999998                              6688887766543444459999999999


Q ss_pred             HHHHHHHhCCCCcCCCcEEEEecCCCCC
Q psy15852        471 SVVIDLLKNPKQKINDKEVDVKKATPKP  498 (661)
Q Consensus       471 e~A~~Ai~~~~~~l~g~~i~v~~a~~~~  498 (661)
                      ++++.||......+++++|.|....+..
T Consensus       341 ~~~~~~i~Asp~~ig~~kl~Veek~~~~  368 (419)
T KOG0116|consen  341 AAVQNAIEASPLEIGGRKLNVEEKRPGF  368 (419)
T ss_pred             chhhhhhhcCccccCCeeEEEEeccccc
Confidence            9999999888999999999997766543

>KOG4210|consensus

Probab=98.09  E-value=6.2e-06  Score=84.07  Aligned_cols=178  Identities=16%  Similarity=0.280  Sum_probs=129.0

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC-CccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK-QKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~-~~~~g~~i~V~~a~~  262 (661)
                      .+++|++++...+.+.++..++..+|.+..+.+........+++++.+.|...+.+..|++... ..+.+..+.......
T Consensus        88 ~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~~  167 (285)
T KOG4210|consen   88 SSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNTR  167 (285)
T ss_pred             cccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccccc
Confidence            4789999999999999999999999988888887777778899999999999999999998865 344555444433332


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCC
Q psy15852        263 KPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDV  342 (661)
Q Consensus       263 k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  342 (661)
                      ...+....                                                                  ..... 
T Consensus       168 ~~~~~~n~------------------------------------------------------------------~~~~~-  180 (285)
T KOG4210|consen  168 RGLRPKNK------------------------------------------------------------------LSRLS-  180 (285)
T ss_pred             ccccccch------------------------------------------------------------------hcccc-
Confidence            21100000                                                                  00000 


Q ss_pred             CccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCC-cCccchhhhhhccCcccccCCc
Q psy15852        343 TGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPS-IRELEIPEAFLTKTTTVPMTTT  421 (661)
Q Consensus       343 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~-~~~~~l~~~f~~~~~~~~~~~~  421 (661)
                                                                ......++...+++. ++.++|+.+|...         
T Consensus       181 ------------------------------------------~~~s~~~~~~~~~~f~~~~d~~~~~~~~~---------  209 (285)
T KOG4210|consen  181 ------------------------------------------SGPSDTIFFVGELDFSLTRDDLKEHFVSS---------  209 (285)
T ss_pred             ------------------------------------------cCccccceeecccccccchHHHhhhccCc---------
Confidence                                                      000111221223333 7777777766665         


Q ss_pred             ccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHhCCCCcCCCcEEEEecCCCCCCC
Q psy15852        422 EHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEP  500 (661)
Q Consensus       422 ~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~~~~~~l~g~~i~v~~a~~~~~~  500 (661)
                                           |+|..++++.++.++..+|||+|.|.....+..++......+.++.+.+....+.+..
T Consensus       210 ---------------------~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  267 (285)
T KOG4210|consen  210 ---------------------GEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEEDEPRPKS  267 (285)
T ss_pred             ---------------------CcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccCCCCccc
Confidence                                 8899999999999999999999999999999999966557788999999888777544

>KOG0533|consensus

Probab=98.08  E-value=3.5e-05  Score=75.78  Aligned_cols=83  Identities=17%  Similarity=0.329  Sum_probs=73.5

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ..+.+|+|.|||+.++++||+++|..||.++.+-+-.++. |.+.|.|-|.|...++|.+|++.. +..++|+.+.+...
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~-G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRA-GRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCC-CCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            3456899999999999999999999999999988888775 899999999999999999999997 68899999999877


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .+...
T Consensus       160 ~~~~~  164 (243)
T KOG0533|consen  160 SSPSQ  164 (243)
T ss_pred             cCccc
Confidence            65543

>KOG4454|consensus

Probab=98.05  E-value=2.2e-06  Score=80.33  Aligned_cols=79  Identities=16%  Similarity=0.281  Sum_probs=68.6

Q ss_pred             hhccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEE
Q psy15852        180 AKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVK  258 (661)
Q Consensus       180 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~  258 (661)
                      +.+.+++|||.|+...++|+-|.++|-+-|+|..|.|+.+++ ++.+ ||||.|.++-+..-|++.+ +..+.++.+.|+
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 AAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRT   82 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhcc
Confidence            345568999999999999999999999999999999998876 5555 9999999999999999987 577888888776


Q ss_pred             ec
Q psy15852        259 KA  260 (661)
Q Consensus       259 ~a  260 (661)
                      +-
T Consensus        83 ~r   84 (267)
T KOG4454|consen   83 LR   84 (267)
T ss_pred             cc
Confidence            53

>KOG4209|consensus

Probab=98.03  E-value=1.3e-05  Score=79.11  Aligned_cols=81  Identities=21%  Similarity=0.371  Sum_probs=75.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      ....+||+|+.+.++.++++..|+.||.|..+.++.++.++.++||+||+|.+.+..++|+...+..+.++.|.|.+...
T Consensus       100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~r~  179 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLKRT  179 (231)
T ss_pred             CCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeeeeee
Confidence            34789999999999999999999999999999999999999999999999999999999999668899999999998776


Q ss_pred             C
Q psy15852        263 K  263 (661)
Q Consensus       263 k  263 (661)
                      .
T Consensus       180 ~  180 (231)
T KOG4209|consen  180 N  180 (231)
T ss_pred             e
Confidence            5

>KOG0129|consensus

Probab=98.01  E-value=5.9e-05  Score=79.73  Aligned_cols=65  Identities=17%  Similarity=0.244  Sum_probs=61.2

Q ss_pred             ccCCCeEEEcCCCCCCCHHHHHHHhh-cCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        590 VEAKNKMVSHPGIVDKITEELKEHFS-KYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       590 ~~~~~~l~v~nlp~~~te~dL~~~F~-~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      .+..++|||+.||--++-+||-.+|. -||.|.+|-|=+|++=+-++|-|-|+|.+...=.+||..
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            45678999999999999999999998 899999999999988899999999999999999999985

>KOG4661|consensus

Probab=98.01  E-value=8.1e-06  Score=86.06  Aligned_cols=78  Identities=18%  Similarity=0.300  Sum_probs=68.5

Q ss_pred             EEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhh
Q psy15852        102 MVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAK  181 (661)
Q Consensus       102 ~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~  181 (661)
                      ++|.+|...+-..+|+.+|++||+|+-.+|+.+..+--.|.|+||++.+.++|.+|    |..|+...|+|+-|.|..++
T Consensus       408 lWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkC----I~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  408 LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKC----IEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             eeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHH----HHHhhhhhhcceeeeeeecc
Confidence            44444545777889999999999999999999988777899999999999999999    99999999999999998876


Q ss_pred             cc
Q psy15852        182 AK  183 (661)
Q Consensus       182 ~~  183 (661)
                      ..
T Consensus       484 NE  485 (940)
T KOG4661|consen  484 NE  485 (940)
T ss_pred             cC
Confidence            43

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=97.95  E-value=3.2e-05  Score=64.98  Aligned_cols=63  Identities=14%  Similarity=0.095  Sum_probs=56.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhc--CCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        594 NKMVSHPGIVDKITEELKEHFSK--YGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       594 ~~l~v~nlp~~~te~dL~~~F~~--~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      ++|.|+|+|...|.++|.+++..  .|...-+.+|.|..++.+.|||||.|.+++.|.+-.+.-|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~   66 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFN   66 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHc
Confidence            68999999999999998888754  4788899999999999999999999999999998776543

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=97.92  E-value=5.1e-05  Score=63.80  Aligned_cols=78  Identities=14%  Similarity=0.201  Sum_probs=65.0

Q ss_pred             CeeEecCCCccCCHHHHHHHHhc--CCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccC----CeEEEE
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQ--FGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIN----DKEVDV  257 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~--~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~----g~~i~V  257 (661)
                      ++|.|+|||...+.++|.+++..  .|....+.++.|..++.+.|||||.|.+++.|.+-.+.. +..+.    .+...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            58999999999999999998865  467788899999999999999999999999999888774 44332    466778


Q ss_pred             EeccC
Q psy15852        258 KKATP  262 (661)
Q Consensus       258 ~~a~~  262 (661)
                      .+|.-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            77764

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4676|consensus

Probab=97.91  E-value=6.9e-06  Score=83.21  Aligned_cols=141  Identities=14%  Similarity=0.196  Sum_probs=109.6

Q ss_pred             EEEEcCC-CcCCHHHHHHHhhcCCCeeEEEEeeCCCC---CCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852        102 MVSHPGI-VHKITEELKEHFSKYGEIENVTLKSDPNT---GRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus       102 ~~~~~~~-~~~te~~L~~~F~~~G~I~~v~l~~~~~t---g~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      +|-+.|+ |+++.++++.||...|+|.+++|+.+...   ......|||.|.+...+..|     +.|.+.++-++.|.|
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~va-----QhLtntvfvdraliv   83 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVA-----QHLTNTVFVDRALIV   83 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHH-----hhhccceeeeeeEEE
Confidence            5656665 59999999999999999999999875432   23455999999999999995     666666666666555


Q ss_pred             hhhhccC-------------------------------------------------------------CeeEecCCCccC
Q psy15852        178 KKAKAKS-------------------------------------------------------------GKIFVGGLSPEM  196 (661)
Q Consensus       178 ~~~~~~~-------------------------------------------------------------~~lfV~nLp~~~  196 (661)
                      .++....                                                             ++++|.+|+..+
T Consensus        84 ~p~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~  163 (479)
T KOG4676|consen   84 RPYGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAA  163 (479)
T ss_pred             EecCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhh
Confidence            3321100                                                             679999999999


Q ss_pred             CHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccC
Q psy15852        197 KDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKIN  251 (661)
Q Consensus       197 te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~  251 (661)
                      ...++-++|..+|+|...++..    +...-+|-+.|....+...|+..++..+.
T Consensus       164 ~l~e~~e~f~r~Gev~ya~~as----k~~s~~c~~sf~~qts~~halr~~gre~k  214 (479)
T KOG4676|consen  164 ILPESGESFERKGEVSYAHTAS----KSRSSSCSHSFRKQTSSKHALRSHGRERK  214 (479)
T ss_pred             cchhhhhhhhhcchhhhhhhhc----cCCCcchhhhHhhhhhHHHHHHhcchhhh
Confidence            9999999999999998887754    33466778999999999999988876554

>KOG0151|consensus

Probab=97.68  E-value=6.5e-05  Score=81.69  Aligned_cols=92  Identities=14%  Similarity=0.164  Sum_probs=76.4

Q ss_pred             ccccceeeeeecCCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCC---CCCCcccEEEEEEeehhhHHHhhHHH
Q psy15852         86 QILRTHFFYIMEAKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDP---NTGRSRGFAFIVFKDTESLEKASVED  161 (661)
Q Consensus        86 ~~~r~~~~~~~~~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~---~tg~srG~afV~F~~~e~A~~A~~~~  161 (661)
                      +..++.-+...++..+++|++|+. .++++.|...|..||+|.+|+|+.-.   ...+.+-|+||-|.+..||++|    
T Consensus       160 ~s~~~gsfDdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era----  235 (877)
T KOG0151|consen  160 PSGRPGSFDDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERA----  235 (877)
T ss_pred             CCCCCCcCCCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHH----
Confidence            334444555667778888888876 99999999999999999999998632   1234677999999999999999    


Q ss_pred             HHHhCCeeecceeehhhhhh
Q psy15852        162 VIAEGNHVINNKKIEAKKAK  181 (661)
Q Consensus       162 ~~~~~~~~i~g~~i~v~~~~  181 (661)
                      +..+++..+.+..++..|.+
T Consensus       236 ~k~lqg~iv~~~e~K~gWgk  255 (877)
T KOG0151|consen  236 LKELQGIIVMEYEMKLGWGK  255 (877)
T ss_pred             HHHhcceeeeeeeeeecccc
Confidence            99999999999999999985

>KOG1995|consensus

Probab=97.67  E-value=0.00013  Score=74.12  Aligned_cols=83  Identities=17%  Similarity=0.213  Sum_probs=73.6

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeE--------EEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCe
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNII--------ETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDK  253 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~--------~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~  253 (661)
                      ...+|||-+||..+++++|.++|.++|.|.        .|+|-++++|+..|+-|.|.|.+...|+.|+.-. +..+.+.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            346899999999999999999999999774        3567788899999999999999999999999886 6788999


Q ss_pred             EEEEEeccCCCC
Q psy15852        254 EVDVKKATPKPE  265 (661)
Q Consensus       254 ~i~V~~a~~k~~  265 (661)
                      .|+|.+|..+..
T Consensus       145 ~ikvs~a~~r~~  156 (351)
T KOG1995|consen  145 TIKVSLAERRTG  156 (351)
T ss_pred             CchhhhhhhccC
Confidence            999999987764

>KOG4209|consensus

Probab=97.64  E-value=4.6e-05  Score=75.15  Aligned_cols=78  Identities=24%  Similarity=0.333  Sum_probs=67.1

Q ss_pred             CCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         99 KNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        99 ~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ..+.+++++.. .++.+++..+|+.||.|..|.|+.++.++++|||+||+|.+.+.+..|     +.+++..|.++.+.|
T Consensus       100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~a-----y~l~gs~i~~~~i~v  174 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEA-----YKLDGSEIPGPAIEV  174 (231)
T ss_pred             CCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHH-----hhcCCccccccccee
Confidence            34455555554 888888999999999999999999999999999999999999999996     449999999999988


Q ss_pred             hhhh
Q psy15852        178 KKAK  181 (661)
Q Consensus       178 ~~~~  181 (661)
                      .+..
T Consensus       175 t~~r  178 (231)
T KOG4209|consen  175 TLKR  178 (231)
T ss_pred             eeee
Confidence            7654

>KOG0151|consensus

Probab=97.61  E-value=9e-05  Score=80.67  Aligned_cols=85  Identities=18%  Similarity=0.381  Sum_probs=73.5

Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCC---CCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEE
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDK---SKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVD  256 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~  256 (661)
                      .|..++|||+||++.++++.|...|..||+|.+++|+.-+   +..+.+.++||.|-+..+|++|++.+ ++.+.++.++
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            4556899999999999999999999999999999988533   23556789999999999999999998 6889999999


Q ss_pred             EEeccCCCC
Q psy15852        257 VKKATPKPE  265 (661)
Q Consensus       257 V~~a~~k~~  265 (661)
                      +.|.+.-.-
T Consensus       251 ~gWgk~V~i  259 (877)
T KOG0151|consen  251 LGWGKAVPI  259 (877)
T ss_pred             ecccccccc
Confidence            999866544

>KOG4849|consensus

Probab=97.60  E-value=0.00013  Score=72.93  Aligned_cols=76  Identities=13%  Similarity=0.223  Sum_probs=65.3

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCC--CeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFG--NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G--~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      .++||+||-|++|++||.+.+...|  .+.++++..++.+|.+||||+|...+..+..+.++.+ ..+|.|+.-.|...
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            4799999999999999999988877  6677888888888999999999999988888888888 47899987666543

>KOG4676|consensus

Probab=97.54  E-value=3e-05  Score=78.69  Aligned_cols=76  Identities=17%  Similarity=0.275  Sum_probs=61.3

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCC---CCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSK---SQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~---g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      -|.|.||.+.++.++++.+|...|+|..+.|......   ....-.|||.|.+...+..|...-+..+-++.|.|.+..
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecC
Confidence            5889999999999999999999999999988763322   334567999999999888887766777777777776543

>KOG2193|consensus

Probab=97.53  E-value=2.2e-05  Score=80.32  Aligned_cols=149  Identities=17%  Similarity=0.225  Sum_probs=114.3

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCC-eeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCe-eecceeehhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGE-IENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH-VINNKKIEAK  178 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~-I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~-~i~g~~i~v~  178 (661)
                      ++.+..|.|.++..+|..+|...-. ...-.|+       -.||+||.+.+...|.+|    +..++++ .+.|+.+.+.
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~-------k~gyafvd~pdq~wa~ka----ie~~sgk~elqGkr~e~~   71 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-------KSGYAFVDCPDQQWANKA----IETLSGKVELQGKRQEVE   71 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceee-------ecceeeccCCchhhhhhh----HHhhchhhhhcCceeecc
Confidence            3444555579999999999976511 1111122       247999999999999999    8888775 6889999888


Q ss_pred             hhhcc---CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEec-cCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCe
Q psy15852        179 KAKAK---SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMP-YDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDK  253 (661)
Q Consensus       179 ~~~~~---~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~-~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~  253 (661)
                      ...++   ++++-|+|+|+...++.|..++.+||.++.|... .+..+    -..-|+|.+.+.++.||..+ ++.+...
T Consensus        72 ~sv~kkqrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~et----avvnvty~~~~~~~~ai~kl~g~Q~en~  147 (584)
T KOG2193|consen   72 HSVPKKQRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSET----AVVNVTYSAQQQHRQAIHKLNGPQLENQ  147 (584)
T ss_pred             chhhHHHHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHH----HHHHHHHHHHHHHHHHHHhhcchHhhhh
Confidence            76554   4789999999999999999999999999998653 33322    22347888999999999987 5788888


Q ss_pred             EEEEEeccCCC
Q psy15852        254 EVDVKKATPKP  264 (661)
Q Consensus       254 ~i~V~~a~~k~  264 (661)
                      .+.|.+.....
T Consensus       148 ~~k~~YiPdeq  158 (584)
T KOG2193|consen  148 HLKVGYIPDEQ  158 (584)
T ss_pred             hhhcccCchhh
Confidence            99998876544

>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=97.37  E-value=0.00036  Score=60.07  Aligned_cols=56  Identities=23%  Similarity=0.265  Sum_probs=37.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhC
Q psy15852        594 NKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED  655 (661)
Q Consensus       594 ~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~  655 (661)
                      .-|.|.+++.+++.++|+++|+.||.|.+|.+.+...      .|+|.|.++++|.+|+++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~   57 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKL   57 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHH
Confidence            3578888999999999999999999999999997554      8999999999999999863

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>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=97.36  E-value=0.00067  Score=54.36  Aligned_cols=68  Identities=9%  Similarity=0.210  Sum_probs=45.7

Q ss_pred             eeEecCCCccCCHHH----HHHHHhcCC-CeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        186 KIFVGGLSPEMKDEE----IKAHFAQFG-NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       186 ~lfV~nLp~~~te~~----L~~~F~~~G-~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                      -|+|.|||.+.+...    |++++..+| .|.+|          ..+.|+|.|.+.+.|.+|.+.+ +..+-|.+|.|++
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            589999999888764    566667787 66554          1467999999999999999998 6788999999998


Q ss_pred             ccCC
Q psy15852        260 ATPK  263 (661)
Q Consensus       260 a~~k  263 (661)
                      ....
T Consensus        74 ~~~~   77 (90)
T PF11608_consen   74 SPKN   77 (90)
T ss_dssp             S--S
T ss_pred             cCCc
Confidence            7543

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.33  E-value=0.00048  Score=51.27  Aligned_cols=52  Identities=25%  Similarity=0.391  Sum_probs=41.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHH
Q psy15852        594 NKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS  652 (661)
Q Consensus       594 ~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~  652 (661)
                      +.|-|.+.|.+..+ +|..+|..||+|..+.+.....      +.+|+|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~~~------~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPESTN------WMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCCCc------EEEEEECCHHHHHhhC
Confidence            45777788876664 4555999999999988884444      8999999999999995

>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=97.24  E-value=0.0005  Score=59.23  Aligned_cols=67  Identities=25%  Similarity=0.412  Sum_probs=42.1

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC------CCccCCeEEEEE
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP------KQKINDKEVDVK  258 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~------~~~~~g~~i~V~  258 (661)
                      -|+|.+++..++.++|++.|++||.|..|.+.+.      ...|||.|.+.++|++|++..      ...+.+..+.+.
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            4788899999999999999999999999999764      335999999999999999874      234555555444

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.95  E-value=0.00078  Score=67.24  Aligned_cols=87  Identities=15%  Similarity=0.304  Sum_probs=62.5

Q ss_pred             EEEEcCCCcCCHHH----H--HHHhhcCCCeeEEEEeeCCCC-CCcccEE--EEEEeehhhHHHhhHHHHHHhCCeeecc
Q psy15852        102 MVSHPGIVHKITEE----L--KEHFSKYGEIENVTLKSDPNT-GRSRGFA--FIVFKDTESLEKASVEDVIAEGNHVINN  172 (661)
Q Consensus       102 ~~~~~~~~~~te~~----L--~~~F~~~G~I~~v~l~~~~~t-g~srG~a--fV~F~~~e~A~~A~~~~~~~~~~~~i~g  172 (661)
                      +.+++++|.+..|+    |  .++|.+||.|..|.|-+...+ ....+.+  ||.|.+.|+|.+|    |.+.++..++|
T Consensus       117 vYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarc----Ia~vDgs~~DG  192 (480)
T COG5175         117 VYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARC----IAEVDGSLLDG  192 (480)
T ss_pred             eEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHH----HHHhccccccC
Confidence            33455556554444    3  479999999998877653211 1122333  9999999999999    99999999999


Q ss_pred             eeehhhhhhccCCeeEecCC
Q psy15852        173 KKIEAKKAKAKSGKIFVGGL  192 (661)
Q Consensus       173 ~~i~v~~~~~~~~~lfV~nL  192 (661)
                      +.|+..+...+-|+-|++|+
T Consensus       193 r~lkatYGTTKYCtsYLRn~  212 (480)
T COG5175         193 RVLKATYGTTKYCTSYLRNA  212 (480)
T ss_pred             ceEeeecCchHHHHHHHcCC
Confidence            99998877666555555555

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.86  E-value=0.0025  Score=47.47  Aligned_cols=52  Identities=27%  Similarity=0.614  Sum_probs=42.5

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHH
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL  243 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al  243 (661)
                      +.|-|.+.+.+..+. +..+|..||+|..+.+.      ....+.+|+|.++.+|++||
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            457788998877755 55588999999999885      23668999999999999985

>KOG1995|consensus

Probab=96.79  E-value=0.0017  Score=66.05  Aligned_cols=83  Identities=16%  Similarity=0.241  Sum_probs=71.6

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCee--------EEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeee
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIE--------NVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVI  170 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~--------~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i  170 (661)
                      ..++++-.++..+++++|.++|.++|.|.        .|+|-+++.|+..||-|.|.|.++..|+.|    +.-+++..+
T Consensus        66 ~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaa----i~~~agkdf  141 (351)
T KOG1995|consen   66 NETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAA----IEWFAGKDF  141 (351)
T ss_pred             cccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhh----hhhhccccc
Confidence            34566666666999999999999999874        377888999999999999999999999999    999999999


Q ss_pred             cceeehhhhhhccCC
Q psy15852        171 NNKKIEAKKAKAKSG  185 (661)
Q Consensus       171 ~g~~i~v~~~~~~~~  185 (661)
                      .+..|+|..+.....
T Consensus       142 ~gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  142 CGNTIKVSLAERRTG  156 (351)
T ss_pred             cCCCchhhhhhhccC
Confidence            999999988876543

>KOG0115|consensus

Probab=96.78  E-value=0.0018  Score=62.86  Aligned_cols=99  Identities=11%  Similarity=0.159  Sum_probs=82.9

Q ss_pred             HHHhCCeeecceeehhhhhhccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHH
Q psy15852        162 VIAEGNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVID  241 (661)
Q Consensus       162 ~~~~~~~~i~g~~i~v~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~  241 (661)
                      -.+|++....++.+.|.++..  ..|+|.||..-++.+.|++-|+.||+|....+..|.. ++..+-++|.|...-.|.+
T Consensus        11 k~eLd~~~~~~~~lr~rfa~~--a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r-~k~t~eg~v~~~~k~~a~~   87 (275)
T KOG0115|consen   11 KRELDGRFPKGRSLRVRFAMH--AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDR-GKPTREGIVEFAKKPNARK   87 (275)
T ss_pred             HHhcCCCCCCCCceEEEeecc--ceEEEEecchhhhhHHHHHhhhhcCccchheeeeccc-ccccccchhhhhcchhHHH
Confidence            557899999999999999876  6899999999999999999999999999887776654 7788889999999999999


Q ss_pred             HHHhC-----CCccCCeEEEEEeccCC
Q psy15852        242 LLKNP-----KQKINDKEVDVKKATPK  263 (661)
Q Consensus       242 Al~~~-----~~~~~g~~i~V~~a~~k  263 (661)
                      |+...     ..+..+++.-|.+....
T Consensus        88 a~rr~~~~g~~~~~~~~p~~VeP~eq~  114 (275)
T KOG0115|consen   88 AARRCREGGFGGTTGGRPVGVEPMEQP  114 (275)
T ss_pred             HHHHhccCccccCCCCCccCCChhhcc
Confidence            98875     24566677766655443

>KOG0112|consensus

Probab=96.77  E-value=0.0017  Score=72.99  Aligned_cols=140  Identities=11%  Similarity=0.123  Sum_probs=94.2

Q ss_pred             CCceEEeCCCCCCCCcHHHHHHHh-hhccccccccEEeecCCCCc-----eeeecccc--c--------cccccccccee
Q psy15852         29 DDRKLFCPLSSYLELDYLQLWQYF-DWVSSSFSENCLLEDSIGKP-----LTVSCSHH--Y--------YLFDQILRTHF   92 (661)
Q Consensus        29 ~~r~lfVg~l~~~~te~~~l~~~F-~~g~~~~~~~~~~~d~~~~~-----~~~~~~~~--~--------~l~~~~~r~~~   92 (661)
                      .-++||+|+|+...++ .+|+..| .+|  .+.++.+-.-.....     +.+....+  .        .+.....++..
T Consensus       371 atrTLf~Gnl~~kl~e-seiR~af~e~g--kve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTE-SEIRPAFDESG--KVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             hhhhhhhcCcccchhh-hhhhhhhhhhc--cccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            3589999999999999 9999999 998  666655433321111     11111111  0        11111111111


Q ss_pred             ee-eecCCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeec
Q psy15852         93 FY-IMEAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVIN  171 (661)
Q Consensus        93 ~~-~~~~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~  171 (661)
                      -. .......+++.++.+.+....|...|..||+|..|.+-..      .-|+||+|.+...|+.|    +..+.+..|.
T Consensus       448 G~~kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg------q~yayi~yes~~~aq~a----~~~~rgap~G  517 (975)
T KOG0112|consen  448 GQPKSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQAA----THDMRGAPLG  517 (975)
T ss_pred             cccccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC------CcceeeecccCccchhh----HHHHhcCcCC
Confidence            11 2234456778888889999999999999999988776542      23999999999999999    8888888886


Q ss_pred             c--eeehhhhhh
Q psy15852        172 N--KKIEAKKAK  181 (661)
Q Consensus       172 g--~~i~v~~~~  181 (661)
                      +  +.+.|.++.
T Consensus       518 ~P~~r~rvdla~  529 (975)
T KOG0112|consen  518 GPPRRLRVDLAS  529 (975)
T ss_pred             CCCccccccccc
Confidence            5  445555554

>KOG2314|consensus

Probab=96.73  E-value=0.0033  Score=67.18  Aligned_cols=70  Identities=23%  Similarity=0.329  Sum_probs=58.8

Q ss_pred             CCCcEEEEcCCCcCCHH-------HHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeee
Q psy15852         98 AKNKMVSHPGIVHKITE-------ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVI  170 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~-------~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i  170 (661)
                      .-+.++++.+.|-+-.+       -|..+|+++|+|..+.++.+.. |.++||.|++|.+..+|+.|    +..+||+.|
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~a----VK~l~G~~l  130 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKA----VKSLNGKRL  130 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHH----HHhccccee
Confidence            45678888888844333       3667899999999999998877 55999999999999999999    999999887


Q ss_pred             cc
Q psy15852        171 NN  172 (661)
Q Consensus       171 ~g  172 (661)
                      .-
T Consensus       131 dk  132 (698)
T KOG2314|consen  131 DK  132 (698)
T ss_pred             cc
Confidence            53

>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=96.50  E-value=0.004  Score=50.00  Aligned_cols=67  Identities=18%  Similarity=0.232  Sum_probs=45.5

Q ss_pred             CcEEEEcCCC-cCCH----HHHHHHhhcCC-CeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecce
Q psy15852        100 NKMVSHPGIV-HKIT----EELKEHFSKYG-EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK  173 (661)
Q Consensus       100 ~~~~~~~~~~-~~te----~~L~~~F~~~G-~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~  173 (661)
                      .++++|.|+| +.+.    .-|+.++..|| .|.+|.          .+.|+|.|.+++.|++|    ...+++..+.|+
T Consensus         2 ~s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA----~KRmegEdVfG~   67 (90)
T PF11608_consen    2 HSLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERA----QKRMEGEDVFGN   67 (90)
T ss_dssp             SEEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHH----HHHHTT--SSSS
T ss_pred             ccEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHH----HHhhcccccccc
Confidence            3578888888 4444    44778888997 576661          25799999999999999    899999999999


Q ss_pred             eehhhhh
Q psy15852        174 KIEAKKA  180 (661)
Q Consensus       174 ~i~v~~~  180 (661)
                      +|.|.+.
T Consensus        68 kI~v~~~   74 (90)
T PF11608_consen   68 KISVSFS   74 (90)
T ss_dssp             --EEESS
T ss_pred             eEEEEEc
Confidence            9988765

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG2193|consensus

Probab=96.48  E-value=0.00069  Score=69.62  Aligned_cols=75  Identities=15%  Similarity=0.358  Sum_probs=58.8

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC--CccCCeEEEEEeccC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK--QKINDKEVDVKKATP  262 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~--~~~~g~~i~V~~a~~  262 (661)
                      +.+|++||.+..+..||+.+|...-.-.+-.++      ...||+||...+...|.+|++.++  ..+.|+++.|....+
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 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFL------VKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCccee------eecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            468999999999999999999764211111111      237899999999999999999984  578999999998887


Q ss_pred             CCC
Q psy15852        263 KPE  265 (661)
Q Consensus       263 k~~  265 (661)
                      +..
T Consensus        76 kkq   78 (584)
T KOG2193|consen   76 KKQ   78 (584)
T ss_pred             HHH
Confidence            654

>KOG2314|consensus

Probab=96.46  E-value=0.0042  Score=66.42  Aligned_cols=64  Identities=25%  Similarity=0.329  Sum_probs=53.1

Q ss_pred             CCeEEEcCCCCC------CCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        593 KNKMVSHPGIVD------KITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       593 ~~~l~v~nlp~~------~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      .+.|+|-|.|.-      .-..-|..+|+++|+|..+.+|.+.. |.++||.|++|.+..+|..|+.++|.
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G  127 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNG  127 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhccc
Confidence            457888888861      12235778999999999999999998 45999999999999999999997553

>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=96.10  E-value=0.032  Score=47.35  Aligned_cols=78  Identities=23%  Similarity=0.343  Sum_probs=52.4

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEE-eccCCC------CCCcCcEEEEEeCCHHHHHHHHHhCCCccCCe-EE
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETE-MPYDKS------KSQRKNFCFITFEHESVVIDLLKNPKQKINDK-EV  255 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~-i~~~~~------~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~-~i  255 (661)
                      ++.|.|=+.|+..+ ..|.+.|++||.|.+.. +.++..      .........|+|+++.+|.+||.+++..+.|. .+
T Consensus         6 ~~wVtVFGfp~~~~-~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~mv   84 (100)
T PF05172_consen    6 ETWVTVFGFPPSAS-NQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLMV   84 (100)
T ss_dssp             CCEEEEE---GGGH-HHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEEE
T ss_pred             CeEEEEEccCHHHH-HHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEEE
Confidence            45677889998844 56788999999998775 111100      01235688999999999999999999989884 55


Q ss_pred             EEEeccC
Q psy15852        256 DVKKATP  262 (661)
Q Consensus       256 ~V~~a~~  262 (661)
                      -|.++.+
T Consensus        85 GV~~~~~   91 (100)
T PF05172_consen   85 GVKPCDP   91 (100)
T ss_dssp             EEEE-HH
T ss_pred             EEEEcHH
Confidence            6777743

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.

>KOG0115|consensus

Probab=96.09  E-value=0.012  Score=57.30  Aligned_cols=60  Identities=18%  Similarity=0.295  Sum_probs=56.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        594 NKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       594 ~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      .-|+|+||..-+.-+.|.+-|+.||+|.+..+..|.. +++.|-++|.|...-.|.+|+..
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r-~k~t~eg~v~~~~k~~a~~a~rr   91 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDR-GKPTREGIVEFAKKPNARKAARR   91 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeeccc-ccccccchhhhhcchhHHHHHHH
Confidence            4599999999999999999999999999999999876 99999999999999999999875

>KOG1855|consensus

Probab=96.08  E-value=0.0056  Score=63.48  Aligned_cols=64  Identities=20%  Similarity=0.309  Sum_probs=54.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeec---CCC--CCc--------ccEEEEEEcCHHHHHHHHHhCC
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSD---PNT--GRS--------RGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d---~~t--g~s--------~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      ..+|++-|||.|-.-+.|.++|+.+|.|.+|+|+..   +..  |.+        +=+|+|+|+..+.|.+|-+.+.
T Consensus       231 srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  231 SRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             cceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            578999999999999999999999999999999965   332  222        3489999999999999988653

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.06  E-value=0.013  Score=58.71  Aligned_cols=79  Identities=19%  Similarity=0.354  Sum_probs=60.8

Q ss_pred             CeeEecCCCccCCHHHH------HHHHhcCCCeEEEEeccCCCCCC-cCc-E-EEEEeCCHHHHHHHHHhC-CCccCCeE
Q psy15852        185 GKIFVGGLSPEMKDEEI------KAHFAQFGNIIETEMPYDKSKSQ-RKN-F-CFITFEHESVVIDLLKNP-KQKINDKE  254 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L------~~~F~~~G~i~~v~i~~~~~~g~-~~g-~-afV~f~~~~~A~~Al~~~-~~~~~g~~  254 (661)
                      +-+||-+||+.+..+++      .++|.+||.|..|.+-+....-. -.+ + .||+|.+.++|.+||.+. +..++||-
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            56899999999877762      57999999999988865432111 112 2 499999999999999997 68899999


Q ss_pred             EEEEeccCC
Q psy15852        255 VDVKKATPK  263 (661)
Q Consensus       255 i~V~~a~~k  263 (661)
                      |+..+...|
T Consensus       195 lkatYGTTK  203 (480)
T COG5175         195 LKATYGTTK  203 (480)
T ss_pred             EeeecCchH
Confidence            998775543

>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=95.32  E-value=0.074  Score=45.16  Aligned_cols=67  Identities=18%  Similarity=0.337  Sum_probs=46.7

Q ss_pred             EEEcCCCcCCHHHHHHHhhcCCCeeEEE-------------EeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCee
Q psy15852        103 VSHPGIVHKITEELKEHFSKYGEIENVT-------------LKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV  169 (661)
Q Consensus       103 ~~~~~~~~~te~~L~~~F~~~G~I~~v~-------------l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~  169 (661)
                      |.|=..|......|.+.|++||.|.+..             +..      ....-.|.|.++.+|.+|     +..||..
T Consensus         9 VtVFGfp~~~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~------~~NWi~I~Y~~~~~A~rA-----L~~NG~i   77 (100)
T PF05172_consen    9 VTVFGFPPSASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPS------GGNWIHITYDNPLSAQRA-----LQKNGTI   77 (100)
T ss_dssp             EEEE---GGGHHHHHHHHHCCS-EECEEGGG----------E-C------CTTEEEEEESSHHHHHHH-----HTTTTEE
T ss_pred             EEEEccCHHHHHHHHHHHHhcceEEEeecccccccccccccCCC------CCCEEEEECCCHHHHHHH-----HHhCCeE
Confidence            4444455557889999999999998875             222      233889999999999995     7889999


Q ss_pred             ecceeeh-hhhh
Q psy15852        170 INNKKIE-AKKA  180 (661)
Q Consensus       170 i~g~~i~-v~~~  180 (661)
                      +.|.-+- |.+.
T Consensus        78 ~~g~~mvGV~~~   89 (100)
T PF05172_consen   78 FSGSLMVGVKPC   89 (100)
T ss_dssp             ETTCEEEEEEE-
T ss_pred             EcCcEEEEEEEc
Confidence            9885443 4443

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

Probab=95.25  E-value=0.027  Score=58.59  Aligned_cols=67  Identities=16%  Similarity=0.289  Sum_probs=50.2

Q ss_pred             CCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeC---CCCCC----------cccEEEEEEeehhhHHHhhHHHHH
Q psy15852         98 AKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSD---PNTGR----------SRGFAFIVFKDTESLEKASVEDVI  163 (661)
Q Consensus        98 ~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~---~~tg~----------srG~afV~F~~~e~A~~A~~~~~~  163 (661)
                      ...++|++-|+| +-.-+.|.++|+.+|.|..|+|+.-   +.+.+          .+-+|+|+|...+.|.+|    ..
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA----~e  304 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKA----RE  304 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHH----HH
Confidence            345666666666 6677999999999999999999864   22211          366899999999999998    55


Q ss_pred             HhCCe
Q psy15852        164 AEGNH  168 (661)
Q Consensus       164 ~~~~~  168 (661)
                      .++..
T Consensus       305 ~~~~e  309 (484)
T KOG1855|consen  305 LLNPE  309 (484)
T ss_pred             hhchh
Confidence            55443

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.19  E-value=0.083  Score=42.60  Aligned_cols=53  Identities=17%  Similarity=0.285  Sum_probs=41.5

Q ss_pred             cCCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHh
Q psy15852         97 EAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA  157 (661)
Q Consensus        97 ~~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A  157 (661)
                      +..+-+|++.-|.++...||.++|+.||.| .|..+.|.       .|||.....+.|..|
T Consensus         6 P~RdHVFhltFPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v   58 (87)
T PF08675_consen    6 PSRDHVFHLTFPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVV   58 (87)
T ss_dssp             -SGCCEEEEE--TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHH
T ss_pred             CCcceEEEEeCchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHH
Confidence            344668899977799999999999999998 67777663       699999999999997

; 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.

>KOG4849|consensus

Probab=95.05  E-value=0.015  Score=58.70  Aligned_cols=77  Identities=12%  Similarity=0.246  Sum_probs=60.8

Q ss_pred             cCCCcEEEEcCC-CcCCHHHHHHHhhcCCC--eeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecce
Q psy15852         97 EAKNKMVSHPGI-VHKITEELKEHFSKYGE--IENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK  173 (661)
Q Consensus        97 ~~~~~~~~~~~~-~~~te~~L~~~F~~~G~--I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~  173 (661)
                      +.++--+|++|+ |.+|++||.+.....|-  |.++++..++.+|+|||||+|...+..+.++-    +..+-.+.|+|+
T Consensus        77 ~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~----MeiLP~k~iHGQ  152 (498)
T KOG4849|consen   77 EGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQT----MEILPTKTIHGQ  152 (498)
T ss_pred             cCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHH----HHhcccceecCC
Confidence            334445566655 58899999999988885  89999999998999999999999998888885    566777888876


Q ss_pred             eehh
Q psy15852        174 KIEA  177 (661)
Q Consensus       174 ~i~v  177 (661)
                      .-.|
T Consensus       153 ~P~V  156 (498)
T KOG4849|consen  153 SPTV  156 (498)
T ss_pred             CCee
Confidence            5433

>KOG3152|consensus

Probab=95.02  E-value=0.017  Score=56.12  Aligned_cols=75  Identities=23%  Similarity=0.282  Sum_probs=60.2

Q ss_pred             CCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCC--------CCcccE----EEEEEeehhhHHHhhHHHHHHh
Q psy15852         99 KNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNT--------GRSRGF----AFIVFKDTESLEKASVEDVIAE  165 (661)
Q Consensus        99 ~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~t--------g~srG~----afV~F~~~e~A~~A~~~~~~~~  165 (661)
                      +.-+||..++| .+.-.-|+++|+.||.|-.|.|-....+        |.++..    |.|+|.+...|.+.    +..|
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~i----Ae~L  148 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRI----AELL  148 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHH----HHHh
Confidence            33467777666 9999999999999999999999877654        333333    56999999999998    8899


Q ss_pred             CCeeecceeehh
Q psy15852        166 GNHVINNKKIEA  177 (661)
Q Consensus       166 ~~~~i~g~~i~v  177 (661)
                      |+..|.|++-..
T Consensus       149 nn~~Iggkk~S~  160 (278)
T KOG3152|consen  149 NNTPIGGKKKSP  160 (278)
T ss_pred             CCCccCCCCCCc
Confidence            999999976543

>KOG2202|consensus

Probab=94.87  E-value=0.0082  Score=58.50  Aligned_cols=61  Identities=26%  Similarity=0.406  Sum_probs=50.3

Q ss_pred             HHHHHHhh-cCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        114 EELKEHFS-KYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       114 ~~L~~~F~-~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      ++|...|+ +||+|++++|..+.. -+-+|-+||.|..+++|++|    +..+|+..+.|++|....
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~-~hl~GNVYV~f~~Ee~ae~a----~~~lnnRw~~G~pi~ae~  144 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLG-DHLVGNVYVKFRSEEDAEAA----LEDLNNRWYNGRPIHAEL  144 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccc-hhhhhhhhhhcccHHHHHHH----HHHHcCccccCCcceeee
Confidence            34444454 999999998887643 46789999999999999999    999999999999887643

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=94.81  E-value=0.07  Score=43.01  Aligned_cols=52  Identities=17%  Similarity=0.217  Sum_probs=40.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhC
Q psy15852        596 MVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED  655 (661)
Q Consensus       596 l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~  655 (661)
                      ||---.|.+|--.||.++|++||.| .|.-+-|-       -|||...+.+.|..|+...
T Consensus        11 VFhltFPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~   62 (87)
T PF08675_consen   11 VFHLTFPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTL   62 (87)
T ss_dssp             EEEEE--TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHH
T ss_pred             EEEEeCchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHh
Confidence            4555588899999999999999999 77777664       5999999999999988753

; 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.

>KOG3973|consensus

Probab=94.64  E-value=0.22  Score=50.54  Aligned_cols=14  Identities=21%  Similarity=0.048  Sum_probs=7.2

Q ss_pred             CCCCCCCCCccccc
Q psy15852        299 GYGGILYKPLLFYE  312 (661)
Q Consensus       299 ~~~~~~~~~~~~~~  312 (661)
                      ..|+++|.++..+.
T Consensus       378 ~GGGggyqqp~~~~  391 (465)
T KOG3973|consen  378 RGGGGGYQQPQQQQ  391 (465)
T ss_pred             CCCCCCCcCchhhh
Confidence            34445566655543

>KOG3152|consensus

Probab=94.28  E-value=0.027  Score=54.78  Aligned_cols=71  Identities=14%  Similarity=0.298  Sum_probs=56.5

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCC--------CCcCc----EEEEEeCCHHHHHHHHHhC-CCc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSK--------SQRKN----FCFITFEHESVVIDLLKNP-KQK  249 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~--------g~~~g----~afV~f~~~~~A~~Al~~~-~~~  249 (661)
                      +..-||+++||+.+.-..|+++|+.||.|-.|.+.....+        |.+..    -+.|+|.+...|..+...+ +..
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            4467999999999999999999999999999998876544        22222    2789999999998887776 456


Q ss_pred             cCCe
Q psy15852        250 INDK  253 (661)
Q Consensus       250 ~~g~  253 (661)
                      |.|+
T Consensus       153 Iggk  156 (278)
T KOG3152|consen  153 IGGK  156 (278)
T ss_pred             cCCC
Confidence            6664

>KOG2591|consensus

Probab=94.24  E-value=0.085  Score=56.71  Aligned_cols=88  Identities=17%  Similarity=0.240  Sum_probs=67.7

Q ss_pred             HHHhCCeeecceeehhhhhhccCCeeEecCCCccCCHHHHHHHHhc--CCCeEEEEeccCCCCCCcCcEEEEEeCCHHHH
Q psy15852        162 VIAEGNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQ--FGNIIETEMPYDKSKSQRKNFCFITFEHESVV  239 (661)
Q Consensus       162 ~~~~~~~~i~g~~i~v~~~~~~~~~lfV~nLp~~~te~~L~~~F~~--~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A  239 (661)
                      +.+.-+..++.+-.+|.. ..+.|-|.++.||..+..|+++.+|+.  +-++.+|.+-.+..       -||+|++..||
T Consensus       154 lresp~VqvDekgekVrp-~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-------WyITfesd~DA  225 (684)
T KOG2591|consen  154 LRESPNVQVDEKGEKVRP-NHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-------WYITFESDTDA  225 (684)
T ss_pred             HhcCCCceeccCcccccc-CcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-------eEEEeecchhH
Confidence            455556666666666643 345577889999999999999999976  66888998865432       79999999999


Q ss_pred             HHHHHhCC---CccCCeEEEE
Q psy15852        240 IDLLKNPK---QKINDKEVDV  257 (661)
Q Consensus       240 ~~Al~~~~---~~~~g~~i~V  257 (661)
                      +.|.+.+.   ++|.|++|..
T Consensus       226 QqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  226 QQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             HHHHHHHHHHHHhhcCcchhh
Confidence            99998873   5788887743

>KOG2135|consensus

Probab=94.22  E-value=0.03  Score=59.00  Aligned_cols=72  Identities=18%  Similarity=0.304  Sum_probs=57.6

Q ss_pred             eEecCCCcc-CCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCCC
Q psy15852        187 IFVGGLSPE-MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKP  264 (661)
Q Consensus       187 lfV~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k~  264 (661)
                      |-+.-.|+. -+-++|...|.+||+|..|.+-..      ---|.|+|.+..+|-+|-+..+..|++|.|+|.|.++..
T Consensus       375 l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  375 LALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             hhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhccccceecCceeEEEEecCCc
Confidence            444444444 345799999999999999988543      334899999999998888888889999999999998743

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=93.75  E-value=0.26  Score=44.57  Aligned_cols=75  Identities=20%  Similarity=0.352  Sum_probs=52.2

Q ss_pred             ccCCeeEecCCC-----c-cCCH---HHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCC
Q psy15852        182 AKSGKIFVGGLS-----P-EMKD---EEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKIND  252 (661)
Q Consensus       182 ~~~~~lfV~nLp-----~-~~te---~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g  252 (661)
                      |...+|.|.=+.     . ...+   .+|.+.|..||++.=+++.-+        .-+|+|.+-++|.+|+...+..++|
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~~v~g   96 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGIQVNG   96 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCSEETT
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHccCCcEECC
Confidence            445677776444     1 2222   367788999999888887643        3789999999999999999999999


Q ss_pred             eEEEEEeccCCC
Q psy15852        253 KEVDVKKATPKP  264 (661)
Q Consensus       253 ~~i~V~~a~~k~  264 (661)
                      +.|.|+...+..
T Consensus        97 ~~l~i~LKtpdW  108 (146)
T PF08952_consen   97 RTLKIRLKTPDW  108 (146)
T ss_dssp             EEEEEEE-----
T ss_pred             EEEEEEeCCccH
Confidence            999999877654

; PDB: 1UFW_A 2DNR_A.

>KOG2202|consensus

Probab=93.68  E-value=0.032  Score=54.50  Aligned_cols=64  Identities=13%  Similarity=0.225  Sum_probs=51.3

Q ss_pred             HHHHHHHh-cCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        199 EEIKAHFA-QFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       199 ~~L~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ++|...|+ +||+|+.+.|..+.. -.-.|-+||.|...++|++|+..+ +..+.|++|...+..-.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~-~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLG-DHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccc-hhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            45555555 899999997766543 345788999999999999999998 68999999999887654

>KOG1996|consensus

Probab=93.30  E-value=0.18  Score=49.95  Aligned_cols=65  Identities=26%  Similarity=0.336  Sum_probs=51.4

Q ss_pred             CHHHHHHHhhcCCCeeEEEEeeCCCCCCc-ccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        112 ITEELKEHFSKYGEIENVTLKSDPNTGRS-RGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       112 te~~L~~~F~~~G~I~~v~l~~~~~tg~s-rG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      -++++++-.++||.|..|.|.-.+.--.. .---||+|...++|.+|    +..+||..+.|+.+...+.
T Consensus       299 lede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA----~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  299 LEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKA----VVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHH----HHhcCCceecceeeeheec
Confidence            45678899999999999988876432211 12379999999999999    9999999999998865443

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=93.14  E-value=0.19  Score=45.39  Aligned_cols=56  Identities=21%  Similarity=0.438  Sum_probs=45.6

Q ss_pred             HHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhhc
Q psy15852        114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKA  182 (661)
Q Consensus       114 ~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~~  182 (661)
                      .+|.+.|..||+|.-|++.-+        .-.|+|.+-++|.+     ++.+++..+.|+.|.|....+
T Consensus        51 ~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALa-----als~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALA-----ALSLDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHH-----HHHGCCSEETTEEEEEEE---
T ss_pred             HHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHH-----HHccCCcEECCEEEEEEeCCc
Confidence            378889999999888888764        47999999999999     589999999999998876554

; PDB: 1UFW_A 2DNR_A.

>KOG1996|consensus

Probab=93.13  E-value=0.23  Score=49.27  Aligned_cols=64  Identities=14%  Similarity=0.181  Sum_probs=50.1

Q ss_pred             HHHHHHHHhcCCCeEEEEeccCCCCCCcCc-EEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        198 DEEIKAHFAQFGNIIETEMPYDKSKSQRKN-FCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       198 e~~L~~~F~~~G~i~~v~i~~~~~~g~~~g-~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ++++++.+.+||.|..|.|...+..-...- -.||+|...++|.+|+-.+ +.+|+||.+...+-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            357888999999999998876653322222 2699999999999999887 689999998877654

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=93.08  E-value=0.38  Score=36.80  Aligned_cols=55  Identities=24%  Similarity=0.430  Sum_probs=43.4

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcC---CCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQF---GNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP  246 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~---G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~  246 (661)
                      ...|+|+++. +++.+||+.+|..|   .....|.++-|..       |-|.|.+.+.|.+||.++
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDtS-------cNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDTS-------CNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCCc-------EEEEECCHHHHHHHHHcC
Confidence            3579999986 47778999999998   1355677775532       789999999999999764

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=92.08  E-value=0.46  Score=42.35  Aligned_cols=70  Identities=11%  Similarity=0.137  Sum_probs=53.3

Q ss_pred             CeeEecCCCccC----CHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        185 GKIFVGGLSPEM----KDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       185 ~~lfV~nLp~~~----te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      .+|.|+=|..++    +...+-..++.||+|.+|.+.-       +..|.|.|.+..+|-+|+.+......|..+.+.|-
T Consensus        87 sTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s~~pgtm~qCsWq  159 (166)
T PF15023_consen   87 STIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQSRAPGTMFQCSWQ  159 (166)
T ss_pred             eeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcCCCCCceEEeecc
Confidence            678887555543    3334455668899999998752       44599999999999999999876777888888875


Q ss_pred             c
Q psy15852        261 T  261 (661)
Q Consensus       261 ~  261 (661)
                      .
T Consensus       160 q  160 (166)
T PF15023_consen  160 Q  160 (166)
T ss_pred             c
Confidence            4

>KOG0921|consensus

Probab=91.72  E-value=1  Score=51.75  Aligned_cols=13  Identities=46%  Similarity=0.557  Sum_probs=5.0

Q ss_pred             CCcccEEEEEEee
Q psy15852        138 GRSRGFAFIVFKD  150 (661)
Q Consensus       138 g~srG~afV~F~~  150 (661)
                      |+.++|+==.|.+
T Consensus       899 g~q~~~~g~kfsd  911 (1282)
T KOG0921|consen  899 GTQRKFAGNKFSD  911 (1282)
T ss_pred             cchhhcccccccc
Confidence            3334444333333

>KOG0921|consensus

Probab=90.71  E-value=2  Score=49.68  Aligned_cols=6  Identities=50%  Similarity=0.761  Sum_probs=2.2

Q ss_pred             CCCCCC
Q psy15852        300 YGGILY  305 (661)
Q Consensus       300 ~~~~~~  305 (661)
                      ||+++|
T Consensus      1203 ygsGGY 1208 (1282)
T KOG0921|consen 1203 YGSGGY 1208 (1282)
T ss_pred             cCCCCC
Confidence            333333

>KOG2135|consensus

Probab=89.98  E-value=0.13  Score=54.53  Aligned_cols=72  Identities=25%  Similarity=0.376  Sum_probs=59.8

Q ss_pred             CCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhhccCCeeEec
Q psy15852        111 KITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKAKSGKIFVG  190 (661)
Q Consensus       111 ~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~~~~~~lfV~  190 (661)
                      -+-++|..+|.+||+|..|.|-....      .|.|+|.+..+|-.|     ....+..|+++.|++.|..+..    +.
T Consensus       385 nt~a~ln~hfA~fG~i~n~qv~~~~~------~a~vTF~t~aeag~a-----~~s~~avlnnr~iKl~whnps~----~t  449 (526)
T KOG2135|consen  385 NTIADLNPHFAQFGEIENIQVDYSSL------HAVVTFKTRAEAGEA-----YASHGAVLNNRFIKLFWHNPSP----VT  449 (526)
T ss_pred             chHhhhhhhhhhcCccccccccCchh------hheeeeeccccccch-----hccccceecCceeEEEEecCCc----cc
Confidence            36789999999999999999877533      699999999999884     6788999999999999988755    66


Q ss_pred             CCCccCC
Q psy15852        191 GLSPEMK  197 (661)
Q Consensus       191 nLp~~~t  197 (661)
                      |+|..-|
T Consensus       450 n~pav~t  456 (526)
T KOG2135|consen  450 NIPAVPT  456 (526)
T ss_pred             CcccCcc
Confidence            7765433

>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=89.41  E-value=0.48  Score=44.95  Aligned_cols=63  Identities=21%  Similarity=0.087  Sum_probs=40.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhc-CCCe---eEEEEeecCCC-CC-cccEEEEEEcCHHHHHHHHHhC
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSK-YGEI---ENVTLKSDPNT-GR-SRGFAFIVFKDTESLEKASVED  655 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~-~G~I---~~v~i~~d~~t-g~-s~G~aFV~F~~~e~A~~A~~~~  655 (661)
                      ..+|.||+||+..||+++++.+++ ++.-   .++.-.....+ .. .-.-|+|.|.+.+++..-+...
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~   75 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRF   75 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHC
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhc
Confidence            569999999999999999999988 7776   45542221111 11 1235999999999977766653

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.

>KOG4285|consensus

Probab=88.79  E-value=0.99  Score=45.28  Aligned_cols=75  Identities=19%  Similarity=0.262  Sum_probs=58.1

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCC-eEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKIND-KEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g-~~i~V~~a~~k  263 (661)
                      .-|-|-++|+.-. ..|..+|++||+|.+....      ..-.+-+|.|.+..+|+|||..++..|+| -.|-|+.+..+
T Consensus       198 ~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALskng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  198 TWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             ceEEEeccCccch-hHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhhcCeeeccceEEeeeecCCH
Confidence            4566668877644 4577899999999877653      23568899999999999999999988887 45778888776


Q ss_pred             CCC
Q psy15852        264 PEP  266 (661)
Q Consensus       264 ~~~  266 (661)
                      ...
T Consensus       271 svi  273 (350)
T KOG4285|consen  271 SVI  273 (350)
T ss_pred             HHh
Confidence            543

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=88.33  E-value=1.9  Score=33.10  Aligned_cols=47  Identities=32%  Similarity=0.456  Sum_probs=39.1

Q ss_pred             EEEcCCCcCCHHHHHHHhhcC----CCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHh
Q psy15852        103 VSHPGIVHKITEELKEHFSKY----GEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA  157 (661)
Q Consensus       103 ~~~~~~~~~te~~L~~~F~~~----G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A  157 (661)
                      +.+....+++.++|+.+|..|    + ...|.++-|.       .|=|.|.+.+.|.+|
T Consensus         8 vhirGvd~lsT~dI~~y~~~y~~~~~-~~~IEWIdDt-------ScNvvf~d~~~A~~A   58 (62)
T PF10309_consen    8 VHIRGVDELSTDDIKAYFSEYFDEEG-PFRIEWIDDT-------SCNVVFKDEETAARA   58 (62)
T ss_pred             EEEEcCCCCCHHHHHHHHHHhcccCC-CceEEEecCC-------cEEEEECCHHHHHHH
Confidence            444456789999999999999    5 4588899875       489999999999998

>KOG2068|consensus

Probab=88.07  E-value=0.21  Score=50.93  Aligned_cols=85  Identities=16%  Similarity=0.300  Sum_probs=61.4

Q ss_pred             EEEcCCCc-CCHHHHH--HHhhcCCCeeEEEEeeCCC----CCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceee
Q psy15852        103 VSHPGIVH-KITEELK--EHFSKYGEIENVTLKSDPN----TGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKI  175 (661)
Q Consensus       103 ~~~~~~~~-~te~~L~--~~F~~~G~I~~v~l~~~~~----tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i  175 (661)
                      .++++.+. ..+..|+  +.|.+||.|..|.+.++..    .+.+- -+||.|...++|..|    +...++..+.|+.+
T Consensus        81 yvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~-s~yITy~~~eda~rc----i~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   81 YVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTC-SVYITYEEEEDADRC----IDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCC-cccccccchHhhhhH----HHHhhhHHhhhhhh
Confidence            34444444 4555554  6899999999999988652    11122 379999999999999    99999999999998


Q ss_pred             hhhhhhccCCeeEecCC
Q psy15852        176 EAKKAKAKSGKIFVGGL  192 (661)
Q Consensus       176 ~v~~~~~~~~~lfV~nL  192 (661)
                      +......+-+..|++|.
T Consensus       156 ka~~gttkycs~~l~~~  172 (327)
T KOG2068|consen  156 KASLGTTKYCSFYLRND  172 (327)
T ss_pred             HHhhCCCcchhHHhhhh
Confidence            87777666555555443

>KOG2591|consensus

Probab=87.19  E-value=1.8  Score=47.06  Aligned_cols=67  Identities=19%  Similarity=0.182  Sum_probs=49.3

Q ss_pred             CCCcEEEEcCCC-cCCHHHHHHHhhc--CCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHh---hHHHHHHhCCeeec
Q psy15852         98 AKNKMVSHPGIV-HKITEELKEHFSK--YGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA---SVEDVIAEGNHVIN  171 (661)
Q Consensus        98 ~~~~~~~~~~~~-~~te~~L~~~F~~--~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A---~~~~~~~~~~~~i~  171 (661)
                      .++++++..-++ .+-+|+++.||+.  |-++.+|..-.+.+       =||+|++..||+.|   |.+.+.++.++.|.
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-------WyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-------WYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-------eEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            367788888888 6678889999965  77899998877543       79999999999998   23334444444443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=85.78  E-value=1.4  Score=39.31  Aligned_cols=55  Identities=31%  Similarity=0.324  Sum_probs=42.8

Q ss_pred             CCeEEEcC----CCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        593 KNKMVSHP----GIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       593 ~~~l~v~n----lp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      -.+|.|+=    +.+..+-+.+.+..+.||+|.+|.+.     |+.  -|.|.|.+...|=+|+..
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----Grq--savVvF~d~~SAC~Av~A  144 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----GRQ--SAVVVFKDITSACKAVSA  144 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----CCc--eEEEEehhhHHHHHHHHh
Confidence            45677754    44444445677888999999999988     444  699999999999999885

>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=84.76  E-value=1.7  Score=35.97  Aligned_cols=24  Identities=17%  Similarity=0.054  Sum_probs=20.7

Q ss_pred             cCCCeEEEcCCCCCCCHHHHHHHh
Q psy15852        591 EAKNKMVSHPGIVDKITEELKEHF  614 (661)
Q Consensus       591 ~~~~~l~v~nlp~~~te~dL~~~F  614 (661)
                      .+.++|.|.|+|...+|++|++..
T Consensus        50 vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen   50 VSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             ccCCEEEEeCCCCCCChhhheeeE
Confidence            346899999999999999999854

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>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=84.07  E-value=1.8  Score=41.11  Aligned_cols=72  Identities=22%  Similarity=0.106  Sum_probs=45.1

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhc-CCCe---eEEEEeeCC-CCC-CcccEEEEEEeehhhHHHhhHHHHHHhCCeeecc
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSK-YGEI---ENVTLKSDP-NTG-RSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN  172 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~-~G~I---~~v~l~~~~-~tg-~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g  172 (661)
                      ..++||+.|||.+||+++.+.++. ++.-   ..+.-.... ... ..-.-|||.|.+.+++..-    +..++++.+.+
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F----~~~~~g~~F~D   82 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEF----RDRFDGHVFVD   82 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHH----HHHCTTEEEE-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHH----HHhcCCcEEEC
Confidence            358899999999999999998877 6665   233311111 111 1223499999999998886    77888988755


Q ss_pred             ee
Q psy15852        173 KK  174 (661)
Q Consensus       173 ~~  174 (661)
                      ..
T Consensus        83 ~k   84 (176)
T PF03467_consen   83 SK   84 (176)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

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.

>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=82.70  E-value=1.2  Score=36.86  Aligned_cols=57  Identities=16%  Similarity=0.430  Sum_probs=40.6

Q ss_pred             EEEEEeehhhHHHhhHHHHHHhCCeee--cceeehhhhh--------------hccCCeeEecCCCccCCHHHHHHHH
Q psy15852        144 AFIVFKDTESLEKASVEDVIAEGNHVI--NNKKIEAKKA--------------KAKSGKIFVGGLSPEMKDEEIKAHF  205 (661)
Q Consensus       144 afV~F~~~e~A~~A~~~~~~~~~~~~i--~g~~i~v~~~--------------~~~~~~lfV~nLp~~~te~~L~~~F  205 (661)
                      |.|+|.+++-|++     +.....+.+  .+..+.|...              ....++|.|.|||...++++|++.+
T Consensus         1 AlITF~e~~VA~~-----i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen    1 ALITFEEEGVAQR-----ILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             CEEEeCcHHHHHH-----HHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeE
Confidence            6899999999999     666655544  4444433221              1223789999999999999998653

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2416|consensus

Probab=81.46  E-value=0.64  Score=50.70  Aligned_cols=59  Identities=17%  Similarity=0.217  Sum_probs=45.2

Q ss_pred             cEEEEcCCC-cCCHHHHHHHhh-cCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCee
Q psy15852        101 KMVSHPGIV-HKITEELKEHFS-KYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV  169 (661)
Q Consensus       101 ~~~~~~~~~-~~te~~L~~~F~-~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~  169 (661)
                      .+|++.|+- -+|.-+|++++. ..|.|++. +| |+    -|-.|||.|.+.++|.+.    ..+|++..
T Consensus       445 nvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-Dk----IKShCyV~yss~eEA~at----r~AlhnV~  505 (718)
T KOG2416|consen  445 NVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-DK----IKSHCYVSYSSVEEAAAT----REALHNVQ  505 (718)
T ss_pred             ceEeeecccccchHHHHHHHHhhccCchHHH-HH-HH----hhcceeEecccHHHHHHH----HHHHhccc
Confidence            467777765 899999999998 66778777 33 22    234799999999999996    77777754

>KOG2068|consensus

Probab=80.73  E-value=0.86  Score=46.64  Aligned_cols=81  Identities=22%  Similarity=0.278  Sum_probs=60.0

Q ss_pred             CeeEecCCCccCCHHHH---HHHHhcCCCeEEEEeccCCCCC-CcC--cEEEEEeCCHHHHHHHHHhC-CCccCCeEEEE
Q psy15852        185 GKIFVGGLSPEMKDEEI---KAHFAQFGNIIETEMPYDKSKS-QRK--NFCFITFEHESVVIDLLKNP-KQKINDKEVDV  257 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L---~~~F~~~G~i~~v~i~~~~~~g-~~~--g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V  257 (661)
                      .-+||-+|+..+..+++   .+.|.+||.|..|.+..+.... ..-  .-++|+|...++|..||... +..++|+.++.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            45778888887665554   3589999999999988766211 111  12799999999999999986 67888888777


Q ss_pred             EeccCCCC
Q psy15852        258 KKATPKPE  265 (661)
Q Consensus       258 ~~a~~k~~  265 (661)
                      .+...+-.
T Consensus       158 ~~gttkyc  165 (327)
T KOG2068|consen  158 SLGTTKYC  165 (327)
T ss_pred             hhCCCcch
Confidence            77666543

>KOG2416|consensus

Probab=80.32  E-value=1.3  Score=48.54  Aligned_cols=72  Identities=14%  Similarity=0.190  Sum_probs=56.1

Q ss_pred             CeeEecCCCccCCHHHHHHHHhc-CCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCc---cCCeEEEEEe
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQ-FGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQK---INDKEVDVKK  259 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~-~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~---~~g~~i~V~~  259 (661)
                      +-|+|.||-.-.|.-+|+.++.+ .|.|++.+|-      +-+..|||.|.+.++|.....+| |..   -+.+.|.+.|
T Consensus       445 nvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmD------kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf  518 (718)
T KOG2416|consen  445 NVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMD------KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADF  518 (718)
T ss_pred             ceEeeecccccchHHHHHHHHhhccCchHHHHHH------HhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeee
Confidence            67999999999999999999994 6677776442      23566999999999999998887 432   3557777777


Q ss_pred             ccC
Q psy15852        260 ATP  262 (661)
Q Consensus       260 a~~  262 (661)
                      ...
T Consensus       519 ~~~  521 (718)
T KOG2416|consen  519 VRA  521 (718)
T ss_pred             cch
Confidence            654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	661
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		8e-20
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-05
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		3e-15
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		3e-05
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-15
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-05
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		5e-15
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		4e-05
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		5e-15
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		4e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		1e-14
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		3e-05
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-14
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-05
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		1e-10
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		2e-09
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		2e-09
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		2e-04
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		2e-09
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		2e-04
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		2e-08
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		2e-07
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		1e-06
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		3e-04
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-06
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-06
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		3e-06
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		5e-06
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		6e-05
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		4e-06
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		4e-05
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		6e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		1e-05
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-05
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		5e-05
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		6e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		8e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		9e-05
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-04
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		1e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		1e-04
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		1e-04
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		3e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		2e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		2e-04
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		2e-04
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		2e-04
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-04
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		2e-04
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-04
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		6e-04
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-04
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		3e-04
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		3e-04
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		3e-04
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		4e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		4e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		4e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		4e-04
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		5e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		5e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		5e-04
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		6e-04

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 95.5 bits (236), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 46/150 (30%), Positives = 84/150 (56%), Gaps = 1/150 (0%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNX 173
           + L+E+F KYG + ++ +  DP TGRSRGF F+ F+   S+++      I +G  VI+  
Sbjct: 18  DNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGK-VIDPK 76
Query: 174 XXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
                        IFVGG+ P+++ +E +  F+Q+G II+ ++  DK   Q + F F+T+
Sbjct: 77  RAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136
Query: 234 EHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           +    V  + +N      D+++++K+A P+
Sbjct: 137 DSADAVDRVCQNKFIDFKDRKIEIKRAEPR 166

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 19/47 (40%), Positives = 31/47 (65%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           D   + L+E+F KYG + ++ +  DP TGRSRGF F+ F+   S+++
Sbjct: 14  DTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 80.1 bits (196), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 41/158 (25%), Positives = 75/158 (47%), Gaps = 6/158 (3%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA------SVEDVIAEGN 167
           E L+ HF ++G + +  +  DPNT RSRGF F+ +   E ++ A       V+  + E  
Sbjct: 21  ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPK 80
Query: 168 HVINNXXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKN 227
             ++               IFVGG+  + ++  ++ +F Q+G I   E+  D+   +++ 
Sbjct: 81  RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG 140
Query: 228 FCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           F F+TF+    V  ++      +N    +V+KA  K E
Sbjct: 141 FAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE 178

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 601 GIVDKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           G + + TEE  L+++F +YG+IE + + +D  +G+ RGFAF+ F D +S++K  ++
Sbjct: 103 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 79.7 bits (195), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 41/158 (25%), Positives = 75/158 (47%), Gaps = 6/158 (3%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA------SVEDVIAEGN 167
           E L+ HF ++G + +  +  DPNT RSRGF F+ +   E ++ A       V+  + E  
Sbjct: 28  ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPK 87
Query: 168 HVINNXXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKN 227
             ++               IFVGG+  + ++  ++ +F Q+G I   E+  D+   +++ 
Sbjct: 88  RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG 147
Query: 228 FCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           F F+TF+    V  ++      +N    +V+KA  K E
Sbjct: 148 FAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE 185

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 601 GIVDKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           G + + TEE  L+++F +YG+IE + + +D  +G+ RGFAF+ F D +S++K  ++
Sbjct: 110 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 79.7 bits (195), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 41/158 (25%), Positives = 75/158 (47%), Gaps = 6/158 (3%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA------SVEDVIAEGN 167
           E L+ HF ++G + +  +  DPNT RSRGF F+ +   E ++ A       V+  + E  
Sbjct: 29  ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPK 88
Query: 168 HVINNXXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKN 227
             ++               IFVGG+  + ++  ++ +F Q+G I   E+  D+   +++ 
Sbjct: 89  RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG 148
Query: 228 FCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           F F+TF+    V  ++      +N    +V+KA  K E
Sbjct: 149 FAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE 186

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 601 GIVDKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           G + + TEE  L+++F +YG+IE + + +D  +G+ RGFAF+ F D +S++K  ++
Sbjct: 111 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 166

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 79.7 bits (195), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 41/158 (25%), Positives = 75/158 (47%), Gaps = 6/158 (3%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA------SVEDVIAEGN 167
           E L+ HF ++G + +  +  DPNT RSRGF F+ +   E ++ A       V+  + E  
Sbjct: 27  ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPK 86
Query: 168 HVINNXXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKN 227
             ++               IFVGG+  + ++  ++ +F Q+G I   E+  D+   +++ 
Sbjct: 87  RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG 146
Query: 228 FCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           F F+TF+    V  ++      +N    +V+KA  K E
Sbjct: 147 FAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE 184

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 601 GIVDKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           G + + TEE  L+++F +YG+IE + + +D  +G+ RGFAF+ F D +S++K  ++
Sbjct: 109 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 164

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 40/156 (25%), Positives = 74/156 (47%), Gaps = 6/156 (3%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA------SVEDVIAEGN 167
           E L+ HF ++G + +  +  DPNT RSRGF F+ +   E ++ A       V+  + E  
Sbjct: 28  ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPK 87
Query: 168 HVINNXXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKN 227
             ++               IFVGG+  + ++  ++ +F Q+G I   E+  D+   +++ 
Sbjct: 88  RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG 147
Query: 228 FCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           F F+TF+    V  ++      +N    +V+KA  K
Sbjct: 148 FAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 183

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 601 GIVDKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           G + + TEE  L+++F +YG+IE + + +D  +G+ RGFAF+ F D +S++K  ++
Sbjct: 110 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 40/156 (25%), Positives = 74/156 (47%), Gaps = 6/156 (3%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA------SVEDVIAEGN 167
           E L+ HF ++G + +  +  DPNT RSRGF F+ +   E ++ A       V+  + E  
Sbjct: 26  ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPK 85
Query: 168 HVINNXXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKN 227
             ++               IFVGG+  + ++  ++ +F Q+G I   E+  D+   +++ 
Sbjct: 86  RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG 145
Query: 228 FCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           F F+TF+    V  ++      +N    +V+KA  K
Sbjct: 146 FAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 181

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 601 GIVDKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           G + + TEE  L+++F +YG+IE + + +D  +G+ RGFAF+ F D +S++K  ++
Sbjct: 108 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 27/47 (57%), Positives = 38/47 (80%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           D   ++LK++F+K+GE+ + T+K DPNTGRSRGF FI+FKD  S+EK
Sbjct: 22  DTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEK 68

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 26/48 (54%), Positives = 39/48 (81%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           D   ++LK++FSK+GE+ + TLK DP TGRSRGF F++FK++ES++K 
Sbjct: 10  DTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV 57

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 45/74 (60%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           IFVGGLSP+  +E+I+ +F  FG +   E+P D   ++R+ FCFITF+ E  V  +++  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 247 KQKINDKEVDVKKA 260
              +   + ++K A
Sbjct: 62  YHNVGLSKCEIKVA 75

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 31/47 (65%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           D   E+++E+F  +GE+E++ L  D  T + RGF FI FK+ E ++K
Sbjct: 10  DTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 56

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 45/74 (60%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           IFVGGLSP+  +E+I+ +F  FG +   E+P D   ++R+ FCFITF+ E  V  +++  
Sbjct: 4   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 63
Query: 247 KQKINDKEVDVKKA 260
              +   + ++K A
Sbjct: 64  YHNVGLSKCEIKVA 77

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 31/47 (65%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           D   E+++E+F  +GE+E++ L  D  T + RGF FI FK+ E ++K
Sbjct: 12  DTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 58

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 47/74 (63%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           IFVGGLS     E++K +F QFG + +  + +DK+ ++ + F F+TFE E +V  + +  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 247 KQKINDKEVDVKKA 260
             +IN+K V+ KKA
Sbjct: 62  FHEINNKMVECKKA 75

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 43/77 (55%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           IFVGG+     + E++ +F +FG + E  M YD  K + + F FITFE E  V   +   
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 247 KQKINDKEVDVKKATPK 263
              I  K+V+VK+A P+
Sbjct: 73  FHDIMGKKVEVKRAEPR 89

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 45/77 (58%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           +FVGGL      E ++++F+Q+G +++  +  DK+ +Q + F F+ F+  + V  +L + 
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 247 KQKINDKEVDVKKATPK 263
              ++ + +D K  TP+
Sbjct: 79  PHTLDGRNIDPKPCTPR 95

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/37 (45%), Positives = 25/37 (67%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKD 644
           E L+ +FS+YGE+ +  +  D  T +SRGF F+ FKD
Sbjct: 31  ETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/122 (27%), Positives = 55/122 (45%), Gaps = 1/122 (0%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA-SVEDVIAEGNHVINN 172
           EE +  F   GEIE+  L  D  TG+S G+ F+ + D +  EKA +  + +      I  
Sbjct: 17  EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKV 76
Query: 173 XXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFIT 232
                         ++V GL   M  +E++  F+Q+G II + +  D+     +   FI 
Sbjct: 77  SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIR 136
Query: 233 FE 234
           F+
Sbjct: 137 FD 138

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/140 (23%), Positives = 63/140 (45%), Gaps = 1/140 (0%)
Query: 96  MEAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLE 155
           M++K  ++ +    +   +E K  F   G+IE+  L  D  TG+S G+ F+ + D    +
Sbjct: 1   MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 156 KA-SVEDVIAEGNHVINNXXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIET 214
           KA +  + +      I                ++V GL   M  +E++  F+Q+G II +
Sbjct: 61  KAINTLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITS 120
Query: 215 EMPYDKSKSQRKNFCFITFE 234
            +  D++    +   FI F+
Sbjct: 121 RILLDQATGVSRGVGFIRFD 140

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 24/67 (35%), Positives = 42/67 (62%), Gaps = 6/67 (8%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + T+E L+E+F ++GE++   +  DP T RSRGF F+ F D     +A V+ V+A+
Sbjct: 32  GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD-----QAGVDKVLAQ 86
Query: 166 GNHVINN 172
             H +++
Sbjct: 87  SRHELDS 93

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 50.1 bits (118), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 23/77 (29%), Positives = 43/77 (55%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           +F+GGLS +   E ++ +F QFG + E  +  D    + + F F+TF  ++ V  +L   
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Query: 247 KQKINDKEVDVKKATPK 263
           + +++ K +D K A P+
Sbjct: 88  RHELDSKTIDPKVAFPR 104

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 18/43 (41%), Positives = 28/43 (65%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           E L+E+F ++GE++   +  DP T RSRGF F+ F D   ++K
Sbjct: 40  EGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 82

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 24/67 (35%), Positives = 42/67 (62%), Gaps = 6/67 (8%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + T+E L+E+F ++GE++   +  DP T RSRGF F+ F D     +A V+ V+A+
Sbjct: 7   GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD-----QAGVDKVLAQ 61
Query: 166 GNHVINN 172
             H +++
Sbjct: 62  SRHELDS 68

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/74 (29%), Positives = 41/74 (55%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           +F+GGLS +   E ++ +F QFG + E  +  D    + + F F+TF  ++ V  +L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 247 KQKINDKEVDVKKA 260
           + +++ K +D K A
Sbjct: 63  RHELDSKTIDPKVA 76

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 18/43 (41%), Positives = 28/43 (65%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
           E L+E+F ++GE++   +  DP T RSRGF F+ F D   ++K
Sbjct: 15  EGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 57

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/125 (23%), Positives = 57/125 (45%), Gaps = 1/125 (0%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA-SVEDVIAEGNHVINN 172
           +EL+  FS  GE+E+  L  D   G S G+ F+ +   +  E+A +  + +   +  I  
Sbjct: 17  DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKV 76
Query: 173 XXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFIT 232
                         +++ GL   M  ++++  F++FG II + +  D++    +   FI 
Sbjct: 77  SYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIR 136
Query: 233 FEHES 237
           F+  S
Sbjct: 137 FDKRS 141

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/125 (23%), Positives = 57/125 (45%), Gaps = 1/125 (0%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA-SVEDVIAEGNHVINN 172
           +EL+  FS  GE+E+  L  D   G S G+ F+ +   +  E+A +  + +   +  I  
Sbjct: 17  DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKV 76
Query: 173 XXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFIT 232
                         +++ GL   M  ++++  F++FG II + +  D++    +   FI 
Sbjct: 77  SYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIR 136
Query: 233 FEHES 237
           F+  S
Sbjct: 137 FDKRS 141

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/53 (43%), Positives = 35/53 (66%), Gaps = 2/53 (3%)
Query: 107 GIVH-KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           G +H  ITE+ L+  F  +G+I+N+ L  D +TGRS+G+ FI F D+E   +A
Sbjct: 11  GSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 21/47 (44%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 606 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ITE+ L+  F  +G+I+N+ L  D +TGRS+G+ FI F D+E   +A
Sbjct: 17  ITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 24/53 (45%), Positives = 34/53 (64%), Gaps = 2/53 (3%)
Query: 107 GIVH-KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           G +H  ITE+ L+  F  +G IE++ L  D  TGRS+G+ FI F D+E  +KA
Sbjct: 32  GSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 22/47 (46%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 606 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ITE+ L+  F  +G IE++ L  D  TGRS+G+ FI F D+E  +KA
Sbjct: 38  ITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 25/82 (30%), Positives = 45/82 (54%), Gaps = 7/82 (8%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF----EHESVVIDL 242
           +FVG LSPE+  E+IK+ FA FG I +  +  D +  + K + F++F    + E+ ++ +
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 243 LKNPKQKINDKEVDVKKATPKP 264
                Q +  +++    AT KP
Sbjct: 78  ---GGQWLGGRQIRTNWATRKP 96

>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 = 45.4 bits (106), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 20/47 (42%), Positives = 30/47 (63%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
           +FVG LSPE+  E+IKA FA FG I +  +  D +  + K + F++F
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/49 (38%), Positives = 33/49 (67%)
Query: 109 VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           ++    +L+E FSKYG I +V++  D  + RSRGFAF+ F++ +  ++A
Sbjct: 25  LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +L+E FSKYG I +V++  D  + RSRGFAF+ F++ +  ++A
Sbjct: 31  DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/49 (38%), Positives = 33/49 (67%)
Query: 109 VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           ++    +L+E FSKYG I +V++  D  + RSRGFAF+ F++ +  ++A
Sbjct: 56  LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +L+E FSKYG I +V++  D  + RSRGFAF+ F++ +  ++A
Sbjct: 62  DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/61 (39%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  K TE+ LKE+FS +GE+  V +K D  TG S+GF F+ F + E+  K   +  + +
Sbjct: 22  GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMID 81
Query: 166 G 166
           G
Sbjct: 82  G 82

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/48 (45%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
           G+  K TE+ LKE+FS +GE+  V +K D  TG S+GF F+ F + E+
Sbjct: 22  GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/49 (38%), Positives = 33/49 (67%)
Query: 109 VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           ++    +L+E FSKYG I +V++  D  + RSRGFAF+ F++ +  ++A
Sbjct: 22  LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 70

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +L+E FSKYG I +V++  D  + RSRGFAF+ F++ +  ++A
Sbjct: 28  DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 70

>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 = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/49 (38%), Positives = 33/49 (67%)
Query: 109 VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           ++    +L+E FSKYG I +V++  D  + RSRGFAF+ F++ +  ++A
Sbjct: 25  LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73

>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 = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +L+E FSKYG I +V++  D  + RSRGFAF+ F++ +  ++A
Sbjct: 31  DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/167 (19%), Positives = 71/167 (42%), Gaps = 13/167 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA--SVEDVIAEGNHV-- 169
           + +++ F+ +G I+++ +  D  T + +GFAF+ ++  E+ + A   +  V+  G ++  
Sbjct: 43  DTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 102
Query: 170 --------INNXXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKS 221
                                    I+V  +  ++ D++IK+ F  FG I    +  D +
Sbjct: 103 GRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPT 162
Query: 222 KSQRKNFCFITFEHESVVIDLLKNPKQ-KINDKEVDVKKATPKPEPF 267
             + K + FI +E      D + +     +  + + V KA   P P 
Sbjct: 163 TGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPL 209

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/60 (36%), Positives = 39/60 (65%), Gaps = 3/60 (5%)
Query: 593 KNKMVSH-PGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +N MV++ P  VD++  +L++ F +YG IE+V +  D  T +SRG+ F+ F+   S ++A
Sbjct: 43  RNLMVNYIPTTVDEV--QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 4/73 (5%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           +FVGGLS +  ++ ++  F+++G I E  +  D+   + + F F+TFE+    ID  K+ 
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN----IDDAKDA 70
Query: 247 KQKINDKEVDVKK 259
              +N K VD ++
Sbjct: 71  MMAMNGKSVDGRQ 83

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 19/48 (39%), Positives = 29/48 (60%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           D   + L++ FSKYG+I  V +  D  T RSRGF F+ F++ +  + A
Sbjct: 23  DTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70

>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 = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 38/77 (49%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           I+VG L      E++K  F+QFG +   ++ YD+   + K F F+  + ESV   + K  
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63
Query: 247 KQKINDKEVDVKKATPK 263
                 + + V +A PK
Sbjct: 64  NTDFMGRTIRVTEANPK 80

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/48 (41%), Positives = 30/48 (62%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           D+  E++ +  S  G + N+ +  DP TGRS+G+AFI F+D ES   A
Sbjct: 14  DQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 33/167 (19%), Positives = 71/167 (42%), Gaps = 13/167 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA--SVEDVIAEGNHV-- 169
           + +++ F+ +G I+++ +  D  T + +GFAF+ ++  E+ + A   +  V+  G ++  
Sbjct: 28  DTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 87
Query: 170 --------INNXXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKS 221
                                    I+V  +  ++ D++IK+ F  FG I    +  D +
Sbjct: 88  GRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPT 147
Query: 222 KSQRKNFCFITFEHESVVIDLLKNPKQ-KINDKEVDVKKATPKPEPF 267
             + K + FI +E      D + +     +  + + V KA   P P 
Sbjct: 148 TGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPL 194

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/48 (41%), Positives = 30/48 (62%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           D+  E++ +  S  G + N+ +  DP TGRS+G+AFI F+D ES   A
Sbjct: 13  DQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

>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 = 43.5 bits (101), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/48 (41%), Positives = 30/48 (62%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           D+  E++ +  S  G + N+ +  DP TGRS+G+AFI F+D ES   A
Sbjct: 15  DQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 30/48 (62%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
           ++VGGL+ E+ D+ + A F  FG+I + ++P D    + + F F+ FE
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 62

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 30/48 (62%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
           ++VGGL+ E+ D+ + A F  FG+I + ++P D    + + F F+ FE
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 57

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 30/48 (62%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
           ++VGGL+ E+ D+ + A F  FG+I + ++P D    + + F F+ FE
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 55

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 30/48 (62%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
           ++VGGL+ E+ D+ + A F  FG+I + ++P D    + + F F+ FE
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 52

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 30/48 (62%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
           ++VGGL+ E+ D+ + A F  FG+I + ++P D    + + F F+ FE
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 113

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 33/171 (19%), Positives = 69/171 (40%), Gaps = 21/171 (12%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLE----------------KA 157
           + +++ F+ +G I+++    D  T + +GFAF+ ++  E+ +                K 
Sbjct: 27  DTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKV 86
Query: 158 SVEDVIAEGNHVINNXXXXXXXXXXXXXXIFVGGLSPEMKDEEIKAHFAQFGNIIETEMP 217
                I +   +I+               I+V  +  ++ D++IK+ F  FG I    + 
Sbjct: 87  GRPSNIGQAQPIIDQLAEEARAFNR----IYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 142
Query: 218 YDKSKSQRKNFCFITFEHESVVIDLLKNPKQ-KINDKEVDVKKATPKPEPF 267
            D +  + K + FI +E      D + +     +  + + V KA   P P 
Sbjct: 143 RDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTPPXPL 193

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 16/48 (33%), Positives = 28/48 (58%)
Query: 110 HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           H     L+++F  +G+IE   + +D  TG+SRG+ F+   D  + E+A
Sbjct: 28  HTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	661
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
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
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.97
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.96
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.96
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.96
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.96
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.96
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.94
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.94
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.93
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.93
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.93
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.93
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.92
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.92
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.92
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.92
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.92
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.91
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.91
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.91
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.91
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.91
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.9
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.9
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.9
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.88
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.87
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.86
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.86
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.86
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.82
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.82
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.74
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.73
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.73
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.72
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.72
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.7
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.69
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.67
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.66
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.65
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.64
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.64
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.64
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.64
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.63
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.63
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.62
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.62
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.62
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.62
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.61
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.61
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.61
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.61
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.61
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.61
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.61
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.61
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.61
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.61
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.6
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.6
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.6
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.6
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.6
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.6
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.6
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.6
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.6
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.59
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.59
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.59
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.59
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.59
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.59
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.58
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.58
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.58
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.58
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.58
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.58
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.58
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.58
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.58
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.58
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.58
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.58
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.58
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.58
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.57
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.57
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.57
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.57
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.57
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.57
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.57
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.57
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.56
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.56
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.56
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.56
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.56
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.56
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.56
2div_A	99	TRNA selenocysteine associated protein; structural	99.56
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.56
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.56
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.55
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.55
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.55
2div_A	99	TRNA selenocysteine associated protein; structural	99.55
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.55
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.55
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.55
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.55
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.55
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.54
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.54
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.54
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.54
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.54
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.54
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.54
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.54
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.54
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.53
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.53
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.53
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.53
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.53
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.53
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.53
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.53
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.53
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.53
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.53
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.53
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.53
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.53
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.53
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.53
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.53
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.53
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.52
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.52
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.52
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.52
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.52
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.52
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.52
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.52
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.52
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.52
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.52
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.51
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.51
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.51
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.51
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.51
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.51
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.51
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.51
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.51
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.51
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.51
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.26
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.51
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.51
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.51
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.5
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.5
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.5
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.5
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.5
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.5
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.5
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.5
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.5
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.5
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.5
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.49
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.49
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.49
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.49
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	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
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.49
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.49
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.49
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.49
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.49
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.49
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.49
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.49
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.49
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.48
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.48
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.48
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.48
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.48
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.48
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.48
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.48
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.48
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.48
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.48
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.48
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.48
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.48
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.48
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.47
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.47
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.47
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.47
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.47
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.47
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.47
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.47
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.46
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.46
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.46
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.46
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.46
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.46
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.46
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.46
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.46
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.46
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.46
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.46
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.46
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.46
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.46
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.46
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.45
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.45
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.45
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.45
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.45
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.45
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.45
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.45
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.45
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.45
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.45
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.45
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.45
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.45
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.44
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.44
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.44
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.44
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.44
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.44
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.44
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.44
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.44
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.44
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.44
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.44
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.44
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.44
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.44
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.44
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.44
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.44
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.43
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.43
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.43
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.43
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.43
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.43
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.42
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.42
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.42
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.41
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.41
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.41
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.41
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.41
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.41
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.4
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.4
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.4
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.4
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.4
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.4
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.4
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.39
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.39
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.39
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.39
1x5p_A	97	Negative elongation factor E; structure genomics,	99.38
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.38
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.38
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.37
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.36
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.36
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.36
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.36
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.03
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.34
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.34
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.34
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.34
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.33
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.33
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.33
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.33
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.33
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.33
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.33
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.32
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.32
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.32
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.32
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.31
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.31
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.31
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.3
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.3
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.3
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.3
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.3
1x5p_A	97	Negative elongation factor E; structure genomics,	99.29
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.29
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.29
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.29
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.27
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.27
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.27
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.27
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.26
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.26
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.25
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.25
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.25
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.24
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.24
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.24
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.24
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.23
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.23
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.23
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.22
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.22
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.2
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.19
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.17
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.14
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.14
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.13
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.13
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.12
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.12
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.12
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.11
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.09
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.05
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.03
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.87
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.87
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.76
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.72
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.66
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.6
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.47
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.38
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.32
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.21
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.21
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.65
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.52
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.46
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.43
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.4
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.27
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.21
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.08
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.86
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.78
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.73
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	95.56
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.27
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	95.13
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.25
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	93.97
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.43
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	91.84
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	91.25
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	90.62

>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=6.5e-35  Score=301.71  Aligned_cols=248  Identities=14%  Similarity=0.199  Sum_probs=202.9

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|+.||+|.+|+|++++.  .++|||||+|.+.++|.+|    + .+++..+.|+.|.|.
T Consensus        41 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~A~~A----~-~~~~~~~~g~~i~v~  113 (292)
T 2ghp_A           41 LTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAA----I-TKTHKVVGQNEIIVS  113 (292)
T ss_dssp             -CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHH----H-TTTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC--CCcEEEEEEECCHHHHHHH----H-HhCCcEeCCcEEEEE
Confidence            44555555556999999999999999999999999875  3689999999999999997    6 689999999999998


Q ss_pred             hhhccCCeeEecCCCccCCHHHHHHHHhcCC-CeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEE
Q psy15852        179 KAKAKSGKIFVGGLSPEMKDEEIKAHFAQFG-NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVD  256 (661)
Q Consensus       179 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G-~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~  256 (661)
                      ++  ..++|||+|||+.+++++|+++|++|| .|..|.++.+.. +.++|||||+|.+.++|.+|++.+ +..+.|+.|.
T Consensus       114 ~~--~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  190 (292)
T 2ghp_A          114 HL--TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLV  190 (292)
T ss_dssp             EC--CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             EC--CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            76  468999999999999999999999999 999999998876 788999999999999999999965 7899999999


Q ss_pred             EEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCC
Q psy15852        257 VKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPP  336 (661)
Q Consensus       257 V~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  336 (661)
                      |.++.++......                                                                  .
T Consensus       191 v~~a~~~~~~~~~------------------------------------------------------------------~  204 (292)
T 2ghp_A          191 TKVSNPLEKSKRT------------------------------------------------------------------D  204 (292)
T ss_dssp             EEECCCC-------------------------------------------------------------------------
T ss_pred             EEECCCCcccccc------------------------------------------------------------------c
Confidence            9999865432000                                                                  0


Q ss_pred             CcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCC-cCccchhhhhhccCcc
Q psy15852        337 LAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPS-IRELEIPEAFLTKTTT  415 (661)
Q Consensus       337 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~-~~~~~l~~~f~~~~~~  415 (661)
                      .                                              ......++++.++.+. +++++|+++|..|   
T Consensus       205 ~----------------------------------------------~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~---  235 (292)
T 2ghp_A          205 S----------------------------------------------ATLEGREIMIRNLSTELLDENLLRESFEGF---  235 (292)
T ss_dssp             ------------------------------------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGG---
T ss_pred             c----------------------------------------------cCCCCceEEEECCCcccCCHHHHHHHHhcc---
Confidence            0                                              0001234566666677 8999999999888   


Q ss_pred             cccCCcccchhhcccccccchhhccCCceeEEeeeccccc-CCcccceEEEEeCChHHHHHHHhCCCCcCCCcEEEEecC
Q psy15852        416 VPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKS-KSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  494 (661)
Q Consensus       416 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~-~~~~~g~aFV~F~~~e~A~~Ai~~~~~~l~g~~i~v~~a  494 (661)
                                                 |.|..+.++.+.. ++.++|||||+|.+.++|.+|+.+++..+.|+.|.|.++
T Consensus       236 ---------------------------G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~~l~g~~~~g~~i~V~~a  288 (292)
T 2ghp_A          236 ---------------------------GSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLA  288 (292)
T ss_dssp             ---------------------------SCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEEC
T ss_pred             ---------------------------CCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHHHhcCCEECCcEEEEEEe
Confidence                                       7799999999877 689999999999999999999977778899999999999


Q ss_pred             CCCC
Q psy15852        495 TPKP  498 (661)
Q Consensus       495 ~~~~  498 (661)
                      .+++
T Consensus       289 ~~k~  292 (292)
T 2ghp_A          289 DKKP  292 (292)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8863

>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=1e-34  Score=298.97  Aligned_cols=243  Identities=13%  Similarity=0.201  Sum_probs=207.1

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      +..++++.++++++++++|+++|++|| |.+|++      ++++|||||+|.++++|.+|    +..+++..+.|++|.|
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A----~~~l~~~~~~g~~i~v   89 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAA----INAFHQSRLRERELSV   89 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHH----HHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHH----HHHcCCCeeCCeEEEE
Confidence            344555555555999999999999999 999988      45789999999999999999    8899999999999999


Q ss_pred             hhhhccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEE
Q psy15852        178 KKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVD  256 (661)
Q Consensus       178 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~  256 (661)
                      .++. ..++|||+|||+.+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+|++.+ +..+.|+.|.
T Consensus        90 ~~~~-~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~  168 (284)
T 3smz_A           90 QLQP-TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLY  168 (284)
T ss_dssp             EECC-CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             EecC-CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            8864 4579999999999999999999999999999999999989999999999999999999999765 7899999999


Q ss_pred             EEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCC
Q psy15852        257 VKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPP  336 (661)
Q Consensus       257 V~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  336 (661)
                      |.++.++......                                                                   
T Consensus       169 v~~a~~~~~~~~~-------------------------------------------------------------------  181 (284)
T 3smz_A          169 VHWTDAGQLTPAL-------------------------------------------------------------------  181 (284)
T ss_dssp             EEECCGGGCCTTT-------------------------------------------------------------------
T ss_pred             EEECCCCCCCccc-------------------------------------------------------------------
Confidence            9998764321000                                                                   


Q ss_pred             CcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCc-CccchhhhhhccCcc
Q psy15852        337 LAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSI-RELEIPEAFLTKTTT  415 (661)
Q Consensus       337 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~-~~~~l~~~f~~~~~~  415 (661)
                                                                       .-..++++.++.+.+ ++++|+++|+.|   
T Consensus       182 -------------------------------------------------~~~~~l~v~nlp~~~~~~~~l~~~f~~~---  209 (284)
T 3smz_A          182 -------------------------------------------------LHSRCLCVDRLPPGFNDVDALCRALSAV---  209 (284)
T ss_dssp             -------------------------------------------------TSCSEEEEECCCTTCCCHHHHHHHTCSS---
T ss_pred             -------------------------------------------------CCccEEEEecCCcccCCHHHHHHHhhCC---
Confidence                                                             001234455444554 889999999888   


Q ss_pred             cccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHh-CCCCcCCCcEEEEecC
Q psy15852        416 VPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK-NPKQKINDKEVDVKKA  494 (661)
Q Consensus       416 ~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~-~~~~~l~g~~i~v~~a  494 (661)
                                                 |.|..+.++.+. +++++|||||+|.+.++|.+|+. +++..++|+.|.|.++
T Consensus       210 ---------------------------G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a  261 (284)
T 3smz_A          210 ---------------------------HSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC  261 (284)
T ss_dssp             ---------------------------SCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             ---------------------------CCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEe
Confidence                                       779999998876 78999999999999999999995 7778899999999999


Q ss_pred             CCCCC
Q psy15852        495 TPKPE  499 (661)
Q Consensus       495 ~~~~~  499 (661)
                      .++..
T Consensus       262 ~~~~~  266 (284)
T 3smz_A          262 APGPP  266 (284)
T ss_dssp             CSSSC
T ss_pred             cCCCc
Confidence            88754

>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=4.2e-34  Score=294.40  Aligned_cols=228  Identities=13%  Similarity=0.153  Sum_probs=195.5

Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                      ....++|||+|||+++++++|+++|++|| |.+|.+      ++++|||||+|.+.++|.+|++.+ +..+.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   91 (284)
T 3smz_A           19 FRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL   91 (284)
T ss_dssp             HHCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEe
Confidence            34568999999999999999999999999 999988      556899999999999999999875 6889999999988


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcc
Q psy15852        260 ATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAE  339 (661)
Q Consensus       260 a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (661)
                      +.+.                                                                            
T Consensus        92 ~~~~----------------------------------------------------------------------------   95 (284)
T 3smz_A           92 QPTD----------------------------------------------------------------------------   95 (284)
T ss_dssp             CCCS----------------------------------------------------------------------------
T ss_pred             cCCC----------------------------------------------------------------------------
Confidence            5421                                                                            


Q ss_pred             cCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccC
Q psy15852        340 VDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMT  419 (661)
Q Consensus       340 ~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~  419 (661)
                                                                       ..+++.++.+.+++++|+++|..+       
T Consensus        96 -------------------------------------------------~~l~v~nlp~~~t~~~l~~~f~~~-------  119 (284)
T 3smz_A           96 -------------------------------------------------ALLCVANLPPSLTQQQFEELVRPF-------  119 (284)
T ss_dssp             -------------------------------------------------CEEEEESCCTTCCHHHHHHHHGGG-------
T ss_pred             -------------------------------------------------CEEEEcCCCCcCCHHHHHHHHHhc-------
Confidence                                                             123444444558899999999888       


Q ss_pred             CcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHH-hCCCCcCCCcEEEEecCCCCC
Q psy15852        420 TTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL-KNPKQKINDKEVDVKKATPKP  498 (661)
Q Consensus       420 ~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai-~~~~~~l~g~~i~v~~a~~~~  498 (661)
                                             |.|..+.++.+..+++++|||||+|.+.++|.+|+ ..++..++|+.|.|.++.+..
T Consensus       120 -----------------------G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~  176 (284)
T 3smz_A          120 -----------------------GSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ  176 (284)
T ss_dssp             -----------------------SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGG
T ss_pred             -----------------------CCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence                                   77999999999999999999999999999999999 677788999999998887541


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCccccccccccCCCCCcccCCCccccc
Q psy15852        499 EPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLF  578 (661)
Q Consensus       499 ~~~~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~  578 (661)
                      ...                                                                             
T Consensus       177 ~~~-----------------------------------------------------------------------------  179 (284)
T 3smz_A          177 LTP-----------------------------------------------------------------------------  179 (284)
T ss_dssp             CCT-----------------------------------------------------------------------------
T ss_pred             CCc-----------------------------------------------------------------------------
Confidence            110                                                                             


Q ss_pred             cCCCCccccccccCCCeEEEcCCCCCC-CHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        579 DQNLRTHYFYIVEAKNKMVSHPGIVDK-ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       579 ~~~~~~~~~~~~~~~~~l~v~nlp~~~-te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                                .....++|||+|||+++ |+++|+++|++||.|.+|+|++++ +|+++|||||+|.+.++|.+|+..++.
T Consensus       180 ----------~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g  248 (284)
T 3smz_A          180 ----------ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADG  248 (284)
T ss_dssp             ----------TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTT
T ss_pred             ----------ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCC
Confidence                      00135789999999995 999999999999999999999997 599999999999999999999998665


Q ss_pred             c
Q psy15852        658 F  658 (661)
Q Consensus       658 ~  658 (661)
                      .
T Consensus       249 ~  249 (284)
T 3smz_A          249 L  249 (284)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=2.5e-34  Score=297.25  Aligned_cols=234  Identities=16%  Similarity=0.205  Sum_probs=189.2

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      ...++|||+|||+++++++|+++|++||+|.+|.++++..+  ++|||||+|.+.++|.+|++..+..+.|+.|.|.++.
T Consensus        39 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~~  116 (292)
T 2ghp_A           39 RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLT  116 (292)
T ss_dssp             ---CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEECC
Confidence            44589999999999999999999999999999999988743  5899999999999999999755789999999998863


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccC
Q psy15852        262 PKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVD  341 (661)
Q Consensus       262 ~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (661)
                      ..                                                                              
T Consensus       117 ~~------------------------------------------------------------------------------  118 (292)
T 2ghp_A          117 EC------------------------------------------------------------------------------  118 (292)
T ss_dssp             SC------------------------------------------------------------------------------
T ss_pred             CC------------------------------------------------------------------------------
Confidence            21                                                                              


Q ss_pred             CCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCCc
Q psy15852        342 VTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTT  421 (661)
Q Consensus       342 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~  421 (661)
                                                                      .+++.++.+.+++++|+++|..+         
T Consensus       119 ------------------------------------------------~l~v~nlp~~~t~~~l~~~f~~~---------  141 (292)
T 2ghp_A          119 ------------------------------------------------TLWMTNFPPSYTQRNIRDLLQDI---------  141 (292)
T ss_dssp             ------------------------------------------------EEEEECCCTTCCHHHHHHHHHHT---------
T ss_pred             ------------------------------------------------EEEEECCCCCCCHHHHHHHHHHh---------
Confidence                                                            23344444558899999999888         


Q ss_pred             ccchhhcccccccchhhccCCc-eeEEeeecccccCCcccceEEEEeCChHHHHHHHh-CCCCcCCCcEEEEecCCCCCC
Q psy15852        422 EHMVLVTGTDMMHMEVTEAVPM-EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK-NPKQKINDKEVDVKKATPKPE  499 (661)
Q Consensus       422 ~~~~~~~~~~~~~~~~~~~~~G-~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~-~~~~~l~g~~i~v~~a~~~~~  499 (661)
                                           | +|..+.++.+.. ++++|||||+|.+.++|.+|+. +++..+.|+.|.|.++.+...
T Consensus       142 ---------------------G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  199 (292)
T 2ghp_A          142 ---------------------NVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK  199 (292)
T ss_dssp             ---------------------TCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC--
T ss_pred             ---------------------CCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcc
Confidence                                 7 799999998876 7889999999999999999996 778899999999998886532


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCccccccccccCCCCCcccCCCcccccc
Q psy15852        500 PFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFD  579 (661)
Q Consensus       500 ~~~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~  579 (661)
                      ....                                                                            
T Consensus       200 ~~~~----------------------------------------------------------------------------  203 (292)
T 2ghp_A          200 SKRT----------------------------------------------------------------------------  203 (292)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccc----------------------------------------------------------------------------
Confidence            2100                                                                            


Q ss_pred             CCCCccccccccCCCeEEEcCCCCC-CCHHHHHHHhhcCCCeeEEEEeecCC-CCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        580 QNLRTHYFYIVEAKNKMVSHPGIVD-KITEELKEHFSKYGEIENVTLKSDPN-TGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       580 ~~~~~~~~~~~~~~~~l~v~nlp~~-~te~dL~~~F~~~G~I~~v~i~~d~~-tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                             .......++|||+|||++ +|+++|+++|++||.|.+|+|++++. ||+++|||||+|.+.++|.+|+ .+|.
T Consensus       204 -------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g  275 (292)
T 2ghp_A          204 -------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNR  275 (292)
T ss_dssp             ----------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTT
T ss_pred             -------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcC
Confidence                   001123578999999999 99999999999999999999999887 7999999999999999999999 7765


Q ss_pred             c
Q psy15852        658 F  658 (661)
Q Consensus       658 ~  658 (661)
                      .
T Consensus       276 ~  276 (292)
T 2ghp_A          276 S  276 (292)
T ss_dssp             E
T ss_pred             C
Confidence            4

>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=3.7e-30  Score=249.52  Aligned_cols=164  Identities=27%  Similarity=0.541  Sum_probs=144.6

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|++++.+|+++|||||+|.+.++|.+|    + ..++..+.|+.|.|.
T Consensus        13 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A----~-~~~~~~~~g~~l~v~   87 (196)
T 1l3k_A           13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA----M-NARPHKVDGRVVEPK   87 (196)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH----H-HTCSCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHH----H-hcCCCEECCEEeeee
Confidence            34555555555999999999999999999999999999999999999999999999997    5 458999999999998


Q ss_pred             hhhcc-----------CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC
Q psy15852        179 KAKAK-----------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK  247 (661)
Q Consensus       179 ~~~~~-----------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~  247 (661)
                      ++.+.           .++|||+|||+++++++|+++|++||.|..|.++.+..++.++|||||+|.+.++|.+|++.++
T Consensus        88 ~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~~~  167 (196)
T 1l3k_A           88 RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY  167 (196)
T ss_dssp             ECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSC
T ss_pred             cccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHhCC
Confidence            87543           2789999999999999999999999999999999998889999999999999999999999888


Q ss_pred             CccCCeEEEEEeccCCCCCC
Q psy15852        248 QKINDKEVDVKKATPKPEPF  267 (661)
Q Consensus       248 ~~~~g~~i~V~~a~~k~~~~  267 (661)
                      ..++|+.|.|.++.++.+..
T Consensus       168 ~~~~G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          168 HTVNGHNCEVRKALSKQEMA  187 (196)
T ss_dssp             CEETTEECEEEECC------
T ss_pred             cEECCEEEEEEecCChhHhc
Confidence            99999999999999987653

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

Probab=99.96  E-value=2.7e-29  Score=247.03  Aligned_cols=162  Identities=23%  Similarity=0.352  Sum_probs=146.4

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      +..+|+|.+|++++|+++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++|    +..+++..+.|+.|.+
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~A----i~~~~~~~~~g~~i~~   89 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA----LDTMNFDVIKGKPVRI   89 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH----HHHHTTCEETTEECEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHH----HHHhhhhhcCCccccc
Confidence            445566666666999999999999999999999999999999999999999999999999    8999999999999998


Q ss_pred             hhhhcc-------CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCc
Q psy15852        178 KKAKAK-------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQK  249 (661)
Q Consensus       178 ~~~~~~-------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~  249 (661)
                      .++...       .++|||+|||+.+++++|+++|++||.|..|+|+++.  +.++|||||+|.+.++|.+|++.+ +..
T Consensus        90 ~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~  167 (213)
T 4f02_A           90 MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGML  167 (213)
T ss_dssp             EECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             ccccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCE
Confidence            776543       3789999999999999999999999999999999875  457999999999999999999876 789


Q ss_pred             cCCeEEEEEeccCCCC
Q psy15852        250 INDKEVDVKKATPKPE  265 (661)
Q Consensus       250 ~~g~~i~V~~a~~k~~  265 (661)
                      |+|++|.|.++.++.+
T Consensus       168 ~~g~~i~V~~a~~~~~  183 (213)
T 4f02_A          168 LNDRKVFVGRFKSRKE  183 (213)
T ss_dssp             ETTEECEEEECCCHHH
T ss_pred             ECCEEEEEEEcCCCcc
Confidence            9999999999987653

>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=2.6e-29  Score=237.04  Aligned_cols=159  Identities=33%  Similarity=0.664  Sum_probs=143.0

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+|+|++++.+|+++|||||+|.++++|++|    +.  +++.+.|+.|.+.+
T Consensus         4 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A----~~--~~~~~~g~~i~v~~   77 (167)
T 2cjk_A            4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV----VK--TQHILDGKVIDPKR   77 (167)
T ss_dssp             GEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHH----HH--SCCEETTEECCCEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHH----Hh--cccccCCeEccccc
Confidence            3444444555999999999999999999999999999999999999999999999998    55  36789999999887


Q ss_pred             hhc-----cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeE
Q psy15852        180 AKA-----KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKE  254 (661)
Q Consensus       180 ~~~-----~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~  254 (661)
                      +.+     ..++|||+|||.++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++..+..++|++
T Consensus        78 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~  157 (167)
T 2cjk_A           78 AIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRK  157 (167)
T ss_dssp             CCCHHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSC
T ss_pred             ccchhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeE
Confidence            653     357999999999999999999999999999999999988899999999999999999999996578999999


Q ss_pred             EEEEeccCCC
Q psy15852        255 VDVKKATPKP  264 (661)
Q Consensus       255 i~V~~a~~k~  264 (661)
                      |.|.++.+++
T Consensus       158 i~V~~a~pk~  167 (167)
T 2cjk_A          158 IEIKRAEPRH  167 (167)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEeecCCCC
Confidence            9999998763

>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=2.1e-28  Score=241.02  Aligned_cols=164  Identities=20%  Similarity=0.392  Sum_probs=146.7

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|.+|    +..+++..+.|+.|.|.
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A----~~~l~~~~~~g~~l~v~  103 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA----LEQMNSVMLGGRNIKVG  103 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHH----HHHHSSCCCC-CCCEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHH----HHHccCCeeCCeeEEEe
Confidence            34566665666999999999999999999999999998899999999999999999998    88899999999999997


Q ss_pred             hhhcc----------------CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHH
Q psy15852        179 KAKAK----------------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDL  242 (661)
Q Consensus       179 ~~~~~----------------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A  242 (661)
                      ++...                .++|||+|||.++++++|+++|++||.|..|.++++..+++++|||||+|.+.++|.+|
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A  183 (216)
T 2qfj_A          104 RPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDA  183 (216)
T ss_dssp             CCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH
T ss_pred             cCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHH
Confidence            65432                37999999999999999999999999999999999988999999999999999999999


Q ss_pred             HHhC-CCccCCeEEEEEeccCCCCC
Q psy15852        243 LKNP-KQKINDKEVDVKKATPKPEP  266 (661)
Q Consensus       243 l~~~-~~~~~g~~i~V~~a~~k~~~  266 (661)
                      ++.+ +..|+|+.|.|.++.++..+
T Consensus       184 ~~~l~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          184 VSSMNLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             HHHHTTCBCSSSBCEEEECSSCSST
T ss_pred             HHHccCCEeCCcEEEEEEecCCCCC
Confidence            9975 78999999999999987654

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

Probab=99.96  E-value=2.6e-28  Score=229.59  Aligned_cols=157  Identities=18%  Similarity=0.312  Sum_probs=143.6

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      ++++.++++++++++|+++|++||+|.+|+|++++. ++++|||||+|.+.++|.+|    +..+++..+.|+.|.|.++
T Consensus         2 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A----~~~l~~~~~~g~~i~v~~~   76 (166)
T 3md3_A            2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIA----LQTLNGKQIENNIVKINWA   76 (166)
T ss_dssp             EEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHH----HHHHTTCEETTEECEEEEC
T ss_pred             EEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHH----HHHcCCCccCCCeeEEEEc
Confidence            455555556999999999999999999999999875 78999999999999999999    8899999999999999887


Q ss_pred             hcc-------CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC
Q psy15852        181 KAK-------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND  252 (661)
Q Consensus       181 ~~~-------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g  252 (661)
                      .+.       .++|||+|||..+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++.+ +..++|
T Consensus        77 ~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  156 (166)
T 3md3_A           77 FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG  156 (166)
T ss_dssp             CCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC
Confidence            544       368999999999999999999999999999999999889999999999999999999999975 789999


Q ss_pred             eEEEEEeccC
Q psy15852        253 KEVDVKKATP  262 (661)
Q Consensus       253 ~~i~V~~a~~  262 (661)
                      ++|.|.++.+
T Consensus       157 ~~i~v~~a~~  166 (166)
T 3md3_A          157 RPLRINWAAK  166 (166)
T ss_dssp             EECEEEESCC
T ss_pred             cEEEEEecCC
Confidence            9999999863

>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=99.96  E-value=2.4e-28  Score=230.49  Aligned_cols=157  Identities=18%  Similarity=0.348  Sum_probs=144.4

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+|++++++.+|+++|||||+|.++++|++|    +..+++..+.|++|.|.+
T Consensus         4 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a----~~~l~~~~~~g~~l~v~~   79 (168)
T 1b7f_A            4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA----IKVLNGITVRNKRLKVSY   79 (168)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHH----HHHHTTCEETTEECEEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHH----HHhcCCCEeCCcEEEEEe
Confidence            4555555556999999999999999999999999988999999999999999999998    888999999999999998


Q ss_pred             hhcc-----CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC-
Q psy15852        180 AKAK-----SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND-  252 (661)
Q Consensus       180 ~~~~-----~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g-  252 (661)
                      +.+.     .++|||+|||..+++++|+++|++||.|..+.++++..++.++|||||+|.+.++|.+|++.+ +..+.| 
T Consensus        80 ~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  159 (168)
T 1b7f_A           80 ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG  159 (168)
T ss_dssp             CCCCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             cCCCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCC
Confidence            8653     479999999999999999999999999999999999888999999999999999999999976 678877 


Q ss_pred             -eEEEEEec
Q psy15852        253 -KEVDVKKA  260 (661)
Q Consensus       253 -~~i~V~~a  260 (661)
                       ++|.|.+|
T Consensus       160 ~~~l~V~~A  168 (168)
T 1b7f_A          160 SQPLSVRLA  168 (168)
T ss_dssp             SSCCEEEEC
T ss_pred             CeEEEEEeC
Confidence             99999886

>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=99.96  E-value=4.3e-28  Score=228.37  Aligned_cols=157  Identities=26%  Similarity=0.423  Sum_probs=143.4

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+|++++++.+|+++|||||+|.++++|++|    +..+++..+.|++|.|.+
T Consensus         3 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a----~~~l~~~~~~g~~l~v~~   78 (167)
T 1fxl_A            3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA----INTLNGLRLQTKTIKVSY   78 (167)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH----HHHHTTCEETTEECEEEE
T ss_pred             ceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHH----HHHcCCCccCCceEEEEe
Confidence            4555555556999999999999999999999999998899999999999999999999    888999999999999988


Q ss_pred             hhcc-----CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCe
Q psy15852        180 AKAK-----SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDK  253 (661)
Q Consensus       180 ~~~~-----~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~  253 (661)
                      +.+.     .++|||+|||..+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+|++.+ +..+.|+
T Consensus        79 ~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  158 (167)
T 1fxl_A           79 ARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA  158 (167)
T ss_dssp             CCCCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             cCCCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCC
Confidence            7654     378999999999999999999999999999999999888999999999999999999999976 6889996


Q ss_pred             E--EEEEec
Q psy15852        254 E--VDVKKA  260 (661)
Q Consensus       254 ~--i~V~~a  260 (661)
                      .  |.|.||
T Consensus       159 ~~~i~v~~A  167 (167)
T 1fxl_A          159 TEPITVKFA  167 (167)
T ss_dssp             SSCCEEEEC
T ss_pred             ccceEEEeC
Confidence            4  888875

>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=99.94  E-value=7e-27  Score=221.92  Aligned_cols=157  Identities=22%  Similarity=0.344  Sum_probs=136.2

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCC--CcccEEEEEEeehhhHHHhhHHHHHHhCCeeec---cee
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTG--RSRGFAFIVFKDTESLEKASVEDVIAEGNHVIN---NKK  174 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg--~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~---g~~  174 (661)
                      .++++.++++++++++|+++|++||+|.+|+|++++.++  +++|||||+|.++++|++|    +..+++..+.   ++.
T Consensus         4 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A----~~~l~~~~~~~~~~~~   79 (175)
T 3nmr_A            4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA----QNALHNMKVLPGMHHP   79 (175)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHH----HHHHTTTCCCTTCSSC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHH----HHHhcCcEEccCCccc
Confidence            445555555699999999999999999999999998876  8999999999999999999    8889987775   566


Q ss_pred             ehhhhhhcc------CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-C
Q psy15852        175 IEAKKAKAK------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-K  247 (661)
Q Consensus       175 i~v~~~~~~------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~  247 (661)
                      +.+.++.+.      .++|||+|||+.+++++|+++|++||.|.+|.++++.. +.++|||||+|.+.++|.+|++.+ +
T Consensus        80 ~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~-g~~~g~afV~f~~~~~A~~A~~~l~g  158 (175)
T 3nmr_A           80 IQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQ  158 (175)
T ss_dssp             CEEEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             eEEccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCC-CCEEEEEEEEECCHHHHHHHHHHhcC
Confidence            666655433      37899999999999999999999999999999999864 899999999999999999999886 4


Q ss_pred             CccC---CeEEEEEecc
Q psy15852        248 QKIN---DKEVDVKKAT  261 (661)
Q Consensus       248 ~~~~---g~~i~V~~a~  261 (661)
                      ..+.   +++|.|.+|.
T Consensus       159 ~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          159 AQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             SCCCTTCSSCCEEEECC
T ss_pred             CcccCCCCCCeEEEecC
Confidence            4444   4999999873

>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=99.94  E-value=2.5e-26  Score=222.48  Aligned_cols=178  Identities=22%  Similarity=0.372  Sum_probs=145.0

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      ..++|||+|||+++++++|+++|++||.|.+|.+++++.++.++|||||+|.+.++|.+|++.++..+.|+.|.|.++.+
T Consensus        12 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~~   91 (196)
T 1l3k_A           12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVS   91 (196)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecccC
Confidence            34799999999999999999999999999999999999999999999999999999999999988999999999999876


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCC
Q psy15852        263 KPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDV  342 (661)
Q Consensus       263 k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  342 (661)
                      +......                                                                   ..    
T Consensus        92 ~~~~~~~-------------------------------------------------------------------~~----  100 (196)
T 1l3k_A           92 REDSQRP-------------------------------------------------------------------GA----  100 (196)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccc-------------------------------------------------------------------cc----
Confidence            5421000                                                                   00    


Q ss_pred             CccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCCcc
Q psy15852        343 TGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTE  422 (661)
Q Consensus       343 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~  422 (661)
                                                                ......+++.++.+.+++++|+++|+.|          
T Consensus       101 ------------------------------------------~~~~~~l~V~nLp~~~t~~~l~~~F~~~----------  128 (196)
T 1l3k_A          101 ------------------------------------------HLTVKKIFVGGIKEDTEEHHLRDYFEQY----------  128 (196)
T ss_dssp             --------------------------------------------CCSEEEEECCTTTCCHHHHHHHHTTT----------
T ss_pred             ------------------------------------------CCCcceEEEeCCCCCCCHHHHHHHHhcC----------
Confidence                                                      0001234555555569999999999888          


Q ss_pred             cchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHhCCCCcCCCcEEEEecCCCCCCCCC
Q psy15852        423 HMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEPFG  502 (661)
Q Consensus       423 ~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~~~~~~l~g~~i~v~~a~~~~~~~~  502 (661)
                                          |.|..+.++.+..+++++|||||+|.+.++|.+|+..++..++|+.|.|.++.++.++..
T Consensus       129 --------------------G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~~~~~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          129 --------------------GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             --------------------SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEECC-------
T ss_pred             --------------------CCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHhCCcEECCEEEEEEecCChhHhcc
Confidence                                789999999999999999999999999999999998888999999999999999877654


Q ss_pred             C
Q psy15852        503 V  503 (661)
Q Consensus       503 ~  503 (661)
                      .
T Consensus       189 ~  189 (196)
T 1l3k_A          189 A  189 (196)
T ss_dssp             -
T ss_pred             c
Confidence            3

>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=99.93  E-value=5.1e-26  Score=215.48  Aligned_cols=152  Identities=18%  Similarity=0.370  Sum_probs=136.9

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcC----C-------CeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCC
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKY----G-------EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGN  167 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~----G-------~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~  167 (661)
                      .+++++.++++++++++|+++|++|    |       +|.++++.+      ++|||||+|.++++|++|    + .+++
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A----~-~~~~   72 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQA----M-AFDG   72 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHH----G-GGTT
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHH----H-HhCC
Confidence            3556666666699999999999999    6       777777754      478999999999999998    7 8999


Q ss_pred             eeecceeehhhhhhcc-----CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHH
Q psy15852        168 HVINNKKIEAKKAKAK-----SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDL  242 (661)
Q Consensus       168 ~~i~g~~i~v~~~~~~-----~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A  242 (661)
                      ..+.|++|.|.++...     .++|||+|||..+++++|+++|++||.|..|.+++++.++.++|||||+|.+.++|.+|
T Consensus        73 ~~~~g~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A  152 (172)
T 2g4b_A           73 IIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA  152 (172)
T ss_dssp             CEETTEECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHH
T ss_pred             cEecCceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHH
Confidence            9999999999987654     47999999999999999999999999999999999988899999999999999999999


Q ss_pred             HHhC-CCccCCeEEEEEecc
Q psy15852        243 LKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       243 l~~~-~~~~~g~~i~V~~a~  261 (661)
                      ++.+ +..++|++|.|.+|.
T Consensus       153 ~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          153 IAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             HHHHTTCEETTEECEEEECC
T ss_pred             HHHcCCCEECCeEEEEEeCC
Confidence            9975 789999999999974

>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=99.93  E-value=1.6e-26  Score=219.81  Aligned_cols=155  Identities=21%  Similarity=0.266  Sum_probs=134.4

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||.|.. .++.+..+++++|||||+|.++++|.+|    + .+++..+.|++|.|.
T Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A----~-~l~g~~~~g~~l~v~   86 (175)
T 1fje_B           13 PFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKA----L-ELTGLKVFGNEIKLE   86 (175)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHH----H-HGGGEEETTEEEEEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHH----H-hcCCCEeCCeEEEEe
Confidence            344455555559999999999999998776 3444556789999999999999999998    6 699999999999999


Q ss_pred             hhhcc-------CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCcc
Q psy15852        179 KAKAK-------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKI  250 (661)
Q Consensus       179 ~~~~~-------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~  250 (661)
                      ++.++       .++|||+|||..+++++|+++|++||.|..+     ..++.++|||||+|.+.++|.+|++.+ +..+
T Consensus        87 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  161 (175)
T 1fje_B           87 KPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI  161 (175)
T ss_dssp             CCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEE
T ss_pred             cCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            88753       3789999999999999999999999998776     445889999999999999999999975 6899


Q ss_pred             CCeEEEEEeccCCC
Q psy15852        251 NDKEVDVKKATPKP  264 (661)
Q Consensus       251 ~g~~i~V~~a~~k~  264 (661)
                      .|+.|.|.++.+++
T Consensus       162 ~g~~i~v~~a~~k~  175 (175)
T 1fje_B          162 DGRSVSLYYTGEKG  175 (175)
T ss_dssp             TTEEEEEEECSSCC
T ss_pred             CCeEEEEEecCCCC
Confidence            99999999998763

>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=99.93  E-value=4.4e-25  Score=207.66  Aligned_cols=79  Identities=20%  Similarity=0.347  Sum_probs=73.1

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      +++|||+|||+++++++|+++|++||.|.+|.+++++.++.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            478999999999999999999999999999999999988999999999999999999999864 6889999999887653

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

Probab=99.93  E-value=1.7e-25  Score=216.89  Aligned_cols=156  Identities=17%  Similarity=0.364  Sum_probs=137.9

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcC----C-------CeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCC
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKY----G-------EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGN  167 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~----G-------~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~  167 (661)
                      .+++++.++++++++++|+++|++|    |       .|.++.+      ++++|||||+|.++++|++|    + .+++
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~A----l-~l~g   72 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQA----M-AFDG   72 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHH----G-GGTT
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHH----H-HhcC
Confidence            3455666666699999999999999    4       5666655      45689999999999999998    7 8999


Q ss_pred             eeecceeehhhhhhc-------------------------cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCC
Q psy15852        168 HVINNKKIEAKKAKA-------------------------KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSK  222 (661)
Q Consensus       168 ~~i~g~~i~v~~~~~-------------------------~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~  222 (661)
                      ..+.|++|.|.++..                         ..++|||+|||..+++++|+++|++||.|..|.+++++.+
T Consensus        73 ~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~  152 (198)
T 2yh0_A           73 IIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSAT  152 (198)
T ss_dssp             EEETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTT
T ss_pred             CEEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCC
Confidence            999999999988753                         2379999999999999999999999999999999999888


Q ss_pred             CCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCCC
Q psy15852        223 SQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKPE  265 (661)
Q Consensus       223 g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~~  265 (661)
                      +.++|||||+|.+.++|.+|++.+ +..++|+.|.|.++.++..
T Consensus       153 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          153 GLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             CSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999999975 7899999999999988653

>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=99.92  E-value=3.6e-25  Score=215.60  Aligned_cols=150  Identities=15%  Similarity=0.187  Sum_probs=128.6

Q ss_pred             CcEEEEcCC-CcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGI-VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~-~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+++|.+|+ +.+++++|+++|++||.|.+|+|+++     ++|||||+|.++++|++|    +..+|+..+.|++|.|.
T Consensus         5 ~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~A----i~~lng~~~~g~~l~v~   75 (205)
T 3tyt_A            5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRA----ITHLNNNFMFGQKMNVC   75 (205)
T ss_dssp             SEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             CEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHH----HHHhCCCEECCceEEEE
Confidence            344444555 38999999999999999999999875     379999999999999999    99999999999999998


Q ss_pred             hhhc------------------------------------------cCCeeEecCCCccCCHHHHHHHHhcCCCe--EEE
Q psy15852        179 KAKA------------------------------------------KSGKIFVGGLSPEMKDEEIKAHFAQFGNI--IET  214 (661)
Q Consensus       179 ~~~~------------------------------------------~~~~lfV~nLp~~~te~~L~~~F~~~G~i--~~v  214 (661)
                      +++.                                          +.++|||+|||+.+++++|+++|++||.|  .++
T Consensus        76 ~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v  155 (205)
T 3tyt_A           76 VSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSV  155 (205)
T ss_dssp             ECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEE
T ss_pred             EccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEE
Confidence            7531                                          12469999999999999999999999999  899


Q ss_pred             EeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCe----EEEEEec
Q psy15852        215 EMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDK----EVDVKKA  260 (661)
Q Consensus       215 ~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~----~i~V~~a  260 (661)
                      +++.+.  +.++|||||+|.+.++|.+||..+ +..+.|+    ++.|++|
T Consensus       156 ~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          156 KVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             EECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             EEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            998775  556799999999999999999987 5677775    5777765

>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=99.92  E-value=1.6e-25  Score=210.89  Aligned_cols=164  Identities=25%  Similarity=0.512  Sum_probs=143.5

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK  263 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k  263 (661)
                      +++|||+|||+++++++|+++|++||.|.+|.+++++.++.++|||||+|.+.++|.+|++. .+.++|+.|.|.++.++
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~i~v~~~~~~   81 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT-QHILDGKVIDPKRAIPR   81 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS-CCEETTEECCCEECCCH
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc-ccccCCeEcccccccch
Confidence            47899999999999999999999999999999999998999999999999999999999996 57899999999887643


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCCC
Q psy15852        264 PEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVT  343 (661)
Q Consensus       264 ~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  343 (661)
                      ...                                                                             
T Consensus        82 ~~~-----------------------------------------------------------------------------   84 (167)
T 2cjk_A           82 DEQ-----------------------------------------------------------------------------   84 (167)
T ss_dssp             HHH-----------------------------------------------------------------------------
T ss_pred             hhc-----------------------------------------------------------------------------
Confidence            210                                                                             


Q ss_pred             ccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCCccc
Q psy15852        344 GVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTEH  423 (661)
Q Consensus       344 ~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~~  423 (661)
                                                                .....+++.++.+.+++++|+++|+.|           
T Consensus        85 ------------------------------------------~~~~~l~V~nlp~~~t~~~l~~~F~~~-----------  111 (167)
T 2cjk_A           85 ------------------------------------------DKTGKIFVGGIGPDVRPKEFEEFFSQW-----------  111 (167)
T ss_dssp             ------------------------------------------HHCEEEEEEEECTTCCHHHHHHHHHTT-----------
T ss_pred             ------------------------------------------cCCCeEEECCCCCCCCHHHHHHHHHhC-----------
Confidence                                                      001234455555568999999999888           


Q ss_pred             chhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHhCCCCcCCCcEEEEecCCCC
Q psy15852        424 MVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK  497 (661)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~~~~~~l~g~~i~v~~a~~~  497 (661)
                                         |.|..+.++.+..+++++|||||+|.+.++|++|+.+++..++|+.|.|.+|.++
T Consensus       112 -------------------G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          112 -------------------GTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             -------------------SCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSCEEEEECCCC
T ss_pred             -------------------ccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeEEEEeecCCC
Confidence                               7799999999999999999999999999999999998778999999999999876

>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=99.92  E-value=1.9e-24  Score=221.91  Aligned_cols=152  Identities=20%  Similarity=0.311  Sum_probs=134.2

Q ss_pred             CCCcEEEEcCCCcCCHHHHH----HHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecce
Q psy15852         98 AKNKMVSHPGIVHKITEELK----EHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK  173 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~----~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~  173 (661)
                      +.++|+|.++++++++++|+    ++|++||.|.+|+|++   ++++||||||+|.+.++|.+|    +..+++..|.|+
T Consensus         8 ~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~   80 (282)
T 3pgw_A            8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA----LRSMQGFPFYDK   80 (282)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHH----HHHhcCCeeCCc
Confidence            34555555555699999976    9999999999999986   588999999999999999999    889999999999


Q ss_pred             eehhhhhhcc----------------------------------------------------------------------
Q psy15852        174 KIEAKKAKAK----------------------------------------------------------------------  183 (661)
Q Consensus       174 ~i~v~~~~~~----------------------------------------------------------------------  183 (661)
                      .|.|.++...                                                                      
T Consensus        81 ~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~  160 (282)
T 3pgw_A           81 PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQ  160 (282)
T ss_pred             EEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCC
Confidence            9999776432                                                                      


Q ss_pred             ----------------------------------------------CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEec
Q psy15852        184 ----------------------------------------------SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMP  217 (661)
Q Consensus       184 ----------------------------------------------~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~  217 (661)
                                                                    .++|||+|||..+++++|+++|++||.|.+|+++
T Consensus       161 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~  240 (282)
T 3pgw_A          161 PPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV  240 (282)
T ss_pred             CCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEe
Confidence                                                          2569999999999999999999999999999998


Q ss_pred             cCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccC-CeEEEEEecc
Q psy15852        218 YDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIN-DKEVDVKKAT  261 (661)
Q Consensus       218 ~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~-g~~i~V~~a~  261 (661)
                      .++     +|||||+|.+.++|.+|++.+ +..+. |+.|.|.|++
T Consensus       241 ~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          241 PGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             cCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            653     689999999999999999987 67888 9999999986

>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=99.92  E-value=2.1e-24  Score=204.72  Aligned_cols=64  Identities=23%  Similarity=0.342  Sum_probs=60.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      .++|||+|||+++|+++|+++|++||.|.+|+|++++. |+++|||||+|.+.++|.+|++.+|.
T Consensus        95 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~-g~~~g~afV~f~~~~~A~~A~~~l~g  158 (175)
T 3nmr_A           95 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQ  158 (175)
T ss_dssp             GSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCC-CCEEEEEEEEECCHHHHHHHHHHhcC
Confidence            46799999999999999999999999999999999964 99999999999999999999998774

>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=99.92  E-value=1.6e-24  Score=215.42  Aligned_cols=152  Identities=14%  Similarity=0.248  Sum_probs=135.3

Q ss_pred             CCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852         98 AKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus        98 ~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ...++++.++++ ++++++|+++|++||+|.+|+|++++     +|||||+|.+.++|++|    +..+++..+.|+.|.
T Consensus        33 ~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~A----i~~l~g~~~~g~~l~  103 (229)
T 2adc_A           33 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLA----MSHLNGHKLHGKPIR  103 (229)
T ss_dssp             CCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHH----HHHHTTCBCSSSBCE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHH----HHHhCCCeECCeEEE
Confidence            345666666667 89999999999999999999999874     78999999999999998    888999999999999


Q ss_pred             hhhhhcc----------------------------------------CCeeEecCCCccCCHHHHHHHHhcCC-CeEEEE
Q psy15852        177 AKKAKAK----------------------------------------SGKIFVGGLSPEMKDEEIKAHFAQFG-NIIETE  215 (661)
Q Consensus       177 v~~~~~~----------------------------------------~~~lfV~nLp~~~te~~L~~~F~~~G-~i~~v~  215 (661)
                      |.++...                                        .++|||+|||..+++++|+++|++|| .|..|.
T Consensus       104 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~  183 (229)
T 2adc_A          104 ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFK  183 (229)
T ss_dssp             EECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEE
T ss_pred             EEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEE
Confidence            9877532                                        36799999999999999999999999 999999


Q ss_pred             eccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccC-CeEEEEEeccCC
Q psy15852        216 MPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIN-DKEVDVKKATPK  263 (661)
Q Consensus       216 i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~-g~~i~V~~a~~k  263 (661)
                      ++.+     .+|||||+|.+.++|.+|++.+ +..+. |+.|.|.|+.++
T Consensus       184 i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          184 FFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             ECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            9653     3789999999999999999976 68888 999999999864

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

Probab=99.91  E-value=1.6e-24  Score=212.90  Aligned_cols=168  Identities=17%  Similarity=0.279  Sum_probs=141.9

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      +.++|||+|||+++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|.+|++.+ +..+.|+.|.+.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            4579999999999999999999999999999999999999999999999999999999999886 578999999999876


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccC
Q psy15852        262 PKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVD  341 (661)
Q Consensus       262 ~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (661)
                      ......                                                                          
T Consensus        94 ~~~~~~--------------------------------------------------------------------------   99 (213)
T 4f02_A           94 RDPSLR--------------------------------------------------------------------------   99 (213)
T ss_dssp             CCTHHH--------------------------------------------------------------------------
T ss_pred             cccccc--------------------------------------------------------------------------
Confidence            532100                                                                          


Q ss_pred             CCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCCc
Q psy15852        342 VTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTT  421 (661)
Q Consensus       342 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~  421 (661)
                                                    .             .-...++|.++.+.+++++|+++|..|         
T Consensus       100 ------------------------------~-------------~~~~~l~v~nl~~~~t~~~l~~~F~~~---------  127 (213)
T 4f02_A          100 ------------------------------K-------------SGVGNIFIKNLDKSIDNKALYDTFSAF---------  127 (213)
T ss_dssp             ------------------------------H-------------HCTTEEEEESCCTTCCHHHHHHHHGGG---------
T ss_pred             ------------------------------c-------------cccccceECCcccccHHHHHHHHHhhc---------
Confidence                                          0             001234555555569999999999888         


Q ss_pred             ccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHh-CCCCcCCCcEEEEecCCCCCC
Q psy15852        422 EHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK-NPKQKINDKEVDVKKATPKPE  499 (661)
Q Consensus       422 ~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~-~~~~~l~g~~i~v~~a~~~~~  499 (661)
                                           |+|..+.++.|.  +.++|||||+|.+.++|++|+. +++..|+|+.|.|.+|.++.+
T Consensus       128 ---------------------G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~~  183 (213)
T 4f02_A          128 ---------------------GNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE  183 (213)
T ss_dssp             ---------------------SCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHHH
T ss_pred             ---------------------CCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCcc
Confidence                                 789999999875  3478999999999999999994 677899999999999987643

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

Probab=99.91  E-value=1.6e-24  Score=210.41  Aligned_cols=150  Identities=14%  Similarity=0.249  Sum_probs=133.9

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .++++.++++ ++++++|+++|++||+|.+|+|++++     +|||||+|.+.++|++|    +..+++..+.|+.|.|.
T Consensus         4 ~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A----~~~l~~~~~~g~~l~v~   74 (198)
T 1qm9_A            4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLA----MSHLNGHKLHGKPIRIT   74 (198)
T ss_dssp             CEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHH----HHHHTTCCCSSCCCEEE
T ss_pred             cEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHH----HHHhCCCeecCeEEEEE
Confidence            4566666666 89999999999999999999999874     78999999999999998    88899999999999998


Q ss_pred             hhhcc----------------------------------------CCeeEecCCCccCCHHHHHHHHhcCC-CeEEEEec
Q psy15852        179 KAKAK----------------------------------------SGKIFVGGLSPEMKDEEIKAHFAQFG-NIIETEMP  217 (661)
Q Consensus       179 ~~~~~----------------------------------------~~~lfV~nLp~~~te~~L~~~F~~~G-~i~~v~i~  217 (661)
                      ++...                                        .++|||+|||..+++++|+++|++|| .|..|.++
T Consensus        75 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~  154 (198)
T 1qm9_A           75 LSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF  154 (198)
T ss_dssp             ECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEES
T ss_pred             EecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEE
Confidence            76532                                        46799999999999999999999999 99999997


Q ss_pred             cCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccC-CeEEEEEeccCC
Q psy15852        218 YDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIN-DKEVDVKKATPK  263 (661)
Q Consensus       218 ~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~-g~~i~V~~a~~k  263 (661)
                      .+     .+|+|||+|.+.++|.+|++.+ +..+. |+.|.|.|+.++
T Consensus       155 ~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          155 QK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             ST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             eC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            54     2799999999999999999976 67888 999999999764

>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=99.91  E-value=7e-24  Score=199.79  Aligned_cols=162  Identities=18%  Similarity=0.253  Sum_probs=139.5

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      .++|||+|||+++++++|+++|++||+|.+|.+++++.++.++|||||+|.+.++|.+|++.+ +..+.|++|.|.++.+
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   82 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   82 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCC
Confidence            478999999999999999999999999999999999888999999999999999999999865 7899999999999876


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCC
Q psy15852        263 KPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDV  342 (661)
Q Consensus       263 k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  342 (661)
                      +....                                                                           
T Consensus        83 ~~~~~---------------------------------------------------------------------------   87 (168)
T 1b7f_A           83 GGESI---------------------------------------------------------------------------   87 (168)
T ss_dssp             CSSTT---------------------------------------------------------------------------
T ss_pred             CcccC---------------------------------------------------------------------------
Confidence            43210                                                                           


Q ss_pred             CccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCCcc
Q psy15852        343 TGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTE  422 (661)
Q Consensus       343 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~  422 (661)
                                                                  -...+++.++.+.+++++|+++|+.+          
T Consensus        88 --------------------------------------------~~~~l~v~nl~~~~t~~~l~~~f~~~----------  113 (168)
T 1b7f_A           88 --------------------------------------------KDTNLYVTNLPRTITDDQLDTIFGKY----------  113 (168)
T ss_dssp             --------------------------------------------TTCEEEEESCCTTCCHHHHHHHHTSS----------
T ss_pred             --------------------------------------------CCCCEEEeCCCCCCCHHHHHHhhhcC----------
Confidence                                                        01123444444558999999999888          


Q ss_pred             cchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHh-CCCCcCCC--cEEEEecC
Q psy15852        423 HMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK-NPKQKIND--KEVDVKKA  494 (661)
Q Consensus       423 ~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~-~~~~~l~g--~~i~v~~a  494 (661)
                                          |.|..+.++.+..+++++|||||+|.+.++|.+|+. +++..+.|  ++|.|.+|
T Consensus       114 --------------------G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          114 --------------------GSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             --------------------SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             --------------------CcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence                                779999999999899999999999999999999995 67788877  89988765

>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=99.91  E-value=4.4e-24  Score=216.56  Aligned_cols=154  Identities=19%  Similarity=0.300  Sum_probs=137.4

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++|+++|+++|++||+|.+|+|.+      ++|||||+|.+.++|.+|    +..+++..+.|+.|.|.+
T Consensus        23 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~A~~A----~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           23 CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIA----KAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             GEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHH----HHHHTTCEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHH----HHHcCCcEECCceeEeee
Confidence            3455555555999999999999999999999965      368999999999999999    888999999999999999


Q ss_pred             hhccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-C-CccC---CeE
Q psy15852        180 AKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-K-QKIN---DKE  254 (661)
Q Consensus       180 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~-~~~~---g~~  254 (661)
                      +.+ .++|||+|||+.+++++|+++|++||.|..|.++.+ .+|+++|||||+|.+.++|.+|+..+ + ..+.   +++
T Consensus        93 a~~-~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~  170 (261)
T 3sde_A           93 ATH-GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRP  170 (261)
T ss_dssp             CCC-SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCB
T ss_pred             ccc-CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCce
Confidence            875 569999999999999999999999999999999998 57999999999999999999999997 3 3444   899


Q ss_pred             EEEEeccCCCC
Q psy15852        255 VDVKKATPKPE  265 (661)
Q Consensus       255 i~V~~a~~k~~  265 (661)
                      |.|.++.+...
T Consensus       171 i~v~~~~~~~~  181 (261)
T 3sde_A          171 VIVEPMEQFDD  181 (261)
T ss_dssp             CEEEECCCEES
T ss_pred             EEEeeccccCc
Confidence            99999987643

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

Probab=99.91  E-value=8.3e-24  Score=198.68  Aligned_cols=164  Identities=16%  Similarity=0.275  Sum_probs=139.1

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ++|||+|||.++++++|+++|++||+|.+|.+++++. ++++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++.++
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 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            5899999999999999999999999999999999875 778999999999999999999665 78999999999998764


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCCC
Q psy15852        264 PEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVT  343 (661)
Q Consensus       264 ~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  343 (661)
                      .....                                                                           
T Consensus        80 ~~~~~---------------------------------------------------------------------------   84 (166)
T 3md3_A           80 QQSSS---------------------------------------------------------------------------   84 (166)
T ss_dssp             CCCCC---------------------------------------------------------------------------
T ss_pred             CCCCC---------------------------------------------------------------------------
Confidence            32100                                                                           


Q ss_pred             ccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCCccc
Q psy15852        344 GVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTEH  423 (661)
Q Consensus       344 ~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~~  423 (661)
                                                                .-...+++.++.+.+++++|+++|+.|           
T Consensus        85 ------------------------------------------~~~~~l~v~nl~~~~t~~~l~~~f~~~-----------  111 (166)
T 3md3_A           85 ------------------------------------------DDTFNLFVGDLNVNVDDETLRNAFKDF-----------  111 (166)
T ss_dssp             ------------------------------------------TTCEEEEEESCCTTCCHHHHHHHHTTS-----------
T ss_pred             ------------------------------------------CCCceEEECCCCCCCCHHHHHHHHhcc-----------
Confidence                                                      001134444444558999999999888           


Q ss_pred             chhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHh-CCCCcCCCcEEEEecCCC
Q psy15852        424 MVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK-NPKQKINDKEVDVKKATP  496 (661)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~-~~~~~l~g~~i~v~~a~~  496 (661)
                                         |.|..+.++.+..++.++|||||+|.+.++|.+|+. +++..++|+.|.|.+|.+
T Consensus       112 -------------------G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          112 -------------------PSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             -------------------TTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             -------------------CCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence                               779999999999999999999999999999999995 777889999999998863

>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=99.90  E-value=2.4e-23  Score=202.69  Aligned_cols=76  Identities=13%  Similarity=0.214  Sum_probs=69.3

Q ss_pred             cCCeeEecCCC-ccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        183 KSGKIFVGGLS-PEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       183 ~~~~lfV~nLp-~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ..++|||+||| +.+++++|+++|++||.|.+|+++++     ++|||||+|.+.++|++|++.+ +..+.|++|.|.++
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            35789999999 89999999999999999999999865     3899999999999999999976 78999999999998


Q ss_pred             cCC
Q psy15852        261 TPK  263 (661)
Q Consensus       261 ~~k  263 (661)
                      ..+
T Consensus        78 ~~~   80 (205)
T 3tyt_A           78 KQP   80 (205)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            753

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

Probab=99.90  E-value=1.6e-23  Score=205.98  Aligned_cols=181  Identities=18%  Similarity=0.338  Sum_probs=145.3

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||.++++++|+++|++||.|.+|.++++..++.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            34589999999999999999999999999999999999888999999999999999999999965 78899999999877


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCccc
Q psy15852        261 TPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEV  340 (661)
Q Consensus       261 ~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (661)
                      ..+....                                                                    +.   
T Consensus       106 ~~~~~~~--------------------------------------------------------------------~~---  114 (216)
T 2qfj_A          106 SNIGQAQ--------------------------------------------------------------------PI---  114 (216)
T ss_dssp             SCCGGGH--------------------------------------------------------------------HH---
T ss_pred             CCccccc--------------------------------------------------------------------hh---
Confidence            6432100                                                                    00   


Q ss_pred             CCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCC
Q psy15852        341 DVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTT  420 (661)
Q Consensus       341 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~  420 (661)
                                                  ......         -......+++.++.+.+++++|+++|+.|        
T Consensus       115 ----------------------------~~~~~~---------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~--------  149 (216)
T 2qfj_A          115 ----------------------------IDQLAE---------EARAFNRIYVASVHQDLSDDDIKSVFEAF--------  149 (216)
T ss_dssp             ----------------------------HHHHHH---------HHTTSCEEEEECCCTTCCHHHHHHHHTTS--------
T ss_pred             ----------------------------hhhhhc---------ccCCCcEEEEeCCCCcCCHHHHHHHHhcc--------
Confidence                                        000000         00112345555555569999999999888        


Q ss_pred             cccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHh-CCCCcCCCcEEEEecCCCCCC
Q psy15852        421 TEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK-NPKQKINDKEVDVKKATPKPE  499 (661)
Q Consensus       421 ~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~-~~~~~l~g~~i~v~~a~~~~~  499 (661)
                                            |+|..+.++.+..+++++|||||+|.+.++|.+|+. +++..++|+.|.|.++.+++.
T Consensus       150 ----------------------G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~  207 (216)
T 2qfj_A          150 ----------------------GKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPM  207 (216)
T ss_dssp             ----------------------SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSS
T ss_pred             ----------------------CCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCC
Confidence                                  789999999999999999999999999999999995 677899999999999988754


Q ss_pred             C
Q psy15852        500 P  500 (661)
Q Consensus       500 ~  500 (661)
                      .
T Consensus       208 ~  208 (216)
T 2qfj_A          208 P  208 (216)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.90  E-value=3.1e-22  Score=205.36  Aligned_cols=80  Identities=23%  Similarity=0.414  Sum_probs=72.2

Q ss_pred             ccCCeeEecCCCccCCHHHHH----HHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIK----AHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVD  256 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~----~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~  256 (661)
                      ...++|||+|||+++++++|+    ++|++||.|.+|.+++   +++++|||||+|.+.++|.+|++.+ +..+.|+.|.
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   83 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   83 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            446899999999999999977    8999999999999986   4788999999999999999999876 6889999999


Q ss_pred             EEeccCCC
Q psy15852        257 VKKATPKP  264 (661)
Q Consensus       257 V~~a~~k~  264 (661)
                      |.++..+.
T Consensus        84 v~~a~~~~   91 (282)
T 3pgw_A           84 IQYAKTDS   91 (282)
T ss_pred             EEEeccCc
Confidence            99997544

>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=99.88  E-value=3e-22  Score=203.06  Aligned_cols=61  Identities=23%  Similarity=0.316  Sum_probs=58.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhC
Q psy15852        594 NKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED  655 (661)
Q Consensus       594 ~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~  655 (661)
                      ++|||+|||+++|+++|+++|++||.|.+|+|++| .+|+++|||||+|.+.++|.+|+..+
T Consensus        97 ~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l  157 (261)
T 3sde_A           97 AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERC  157 (261)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHh
Confidence            36999999999999999999999999999999999 57999999999999999999999985

>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=99.87  E-value=5.3e-22  Score=187.71  Aligned_cols=158  Identities=14%  Similarity=0.245  Sum_probs=132.6

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcC----C-------CeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQF----G-------NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKIN  251 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~----G-------~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~  251 (661)
                      +.++|||+|||+++++++|+++|++|    |       .|.++.+.      .++|||||+|.+.++|.+|+...+..+.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~~~~~~~~~   76 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAMAFDGIIFQ   76 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHGGGTTCEET
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHHHhCCcEec
Confidence            35799999999999999999999999    7       78888874      4589999999999999999955578999


Q ss_pred             CeEEEEEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCC
Q psy15852        252 DKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMV  331 (661)
Q Consensus       252 g~~i~V~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  331 (661)
                      |+.|.|.++.......                                                                
T Consensus        77 g~~i~v~~~~~~~~~~----------------------------------------------------------------   92 (172)
T 2g4b_A           77 GQSLKIRRPHDYQPLP----------------------------------------------------------------   92 (172)
T ss_dssp             TEECEEECCSSCCCCT----------------------------------------------------------------
T ss_pred             CceeeecCCcccCCCC----------------------------------------------------------------
Confidence            9999999876432110                                                                


Q ss_pred             CCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhc
Q psy15852        332 QATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLT  411 (661)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~  411 (661)
                                                                             -...+++.++.+.+++++|+++|+.
T Consensus        93 -------------------------------------------------------~~~~l~v~nlp~~~t~~~l~~~f~~  117 (172)
T 2g4b_A           93 -------------------------------------------------------GAHKLFIGGLPNYLNDDQVKELLTS  117 (172)
T ss_dssp             -------------------------------------------------------TTTCEEEECCCTTCCHHHHHHHHHT
T ss_pred             -------------------------------------------------------CCCEEEEEcCCCcCCHHHHHHHHHh
Confidence                                                                   0113444544455899999999988


Q ss_pred             cCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHh-CCCCcCCCcEEE
Q psy15852        412 KTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK-NPKQKINDKEVD  490 (661)
Q Consensus       412 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~-~~~~~l~g~~i~  490 (661)
                      |                              |.|..+.++.+..+++++|||||+|.+.++|++|+. +++..++|+.|.
T Consensus       118 ~------------------------------G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  167 (172)
T 2g4b_A          118 F------------------------------GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL  167 (172)
T ss_dssp             T------------------------------SCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECE
T ss_pred             c------------------------------CCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEE
Confidence            8                              779999999999999999999999999999999995 677889999999


Q ss_pred             EecCC
Q psy15852        491 VKKAT  495 (661)
Q Consensus       491 v~~a~  495 (661)
                      |.+|.
T Consensus       168 V~~As  172 (172)
T 2g4b_A          168 VQRAS  172 (172)
T ss_dssp             EEECC
T ss_pred             EEeCC
Confidence            98874

>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=99.86  E-value=7.9e-21  Score=188.67  Aligned_cols=79  Identities=13%  Similarity=0.303  Sum_probs=71.5

Q ss_pred             hccCCeeEecCCCc-cCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEE
Q psy15852        181 KAKSGKIFVGGLSP-EMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVK  258 (661)
Q Consensus       181 ~~~~~~lfV~nLp~-~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~  258 (661)
                      .+..++|||+|||+ ++++++|+++|++||.|.+|.+++++     +|||||+|.+.++|.+|++.+ +..+.|+.|.|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~  105 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT  105 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34568999999999 99999999999999999999999864     789999999999999999865 789999999999


Q ss_pred             eccCCC
Q psy15852        259 KATPKP  264 (661)
Q Consensus       259 ~a~~k~  264 (661)
                      ++..+.
T Consensus       106 ~a~~~~  111 (229)
T 2adc_A          106 LSKHQN  111 (229)
T ss_dssp             CCSCCC
T ss_pred             EecCcc
Confidence            987653

>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=99.86  E-value=2.2e-22  Score=191.12  Aligned_cols=164  Identities=20%  Similarity=0.259  Sum_probs=132.5

Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      ....++|||+|||.++++++|+++|++||.+.. .++.+..++.++|||||+|.+.++|.+|++..+..+.|+.|.|.++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecC
Confidence            345689999999999999999999999997766 3445556688999999999999999999975578999999999998


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCccc
Q psy15852        261 TPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEV  340 (661)
Q Consensus       261 ~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (661)
                      .++.....                                                                        
T Consensus        89 ~~~~~~~~------------------------------------------------------------------------   96 (175)
T 1fje_B           89 KGRDSKKV------------------------------------------------------------------------   96 (175)
T ss_dssp             CCSSCSTT------------------------------------------------------------------------
T ss_pred             CCcccccc------------------------------------------------------------------------
Confidence            76432100                                                                        


Q ss_pred             CCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCC
Q psy15852        341 DVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTT  420 (661)
Q Consensus       341 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~  420 (661)
                                                                   .-...+++.++.+.+++++|+++|+.+        
T Consensus        97 ---------------------------------------------~~~~~l~v~nlp~~~t~~~l~~~F~~~--------  123 (175)
T 1fje_B           97 ---------------------------------------------RAARTLLAKNLSFNITEDELKEVFEDA--------  123 (175)
T ss_dssp             ---------------------------------------------GGGGEEEEESCCSSCCHHHHHHHCTTC--------
T ss_pred             ---------------------------------------------ccCCEEEEeCCCCCCCHHHHHHHHHhc--------
Confidence                                                         001234455444559999999999887        


Q ss_pred             cccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHh-CCCCcCCCcEEEEecCCCC
Q psy15852        421 TEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK-NPKQKINDKEVDVKKATPK  497 (661)
Q Consensus       421 ~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~-~~~~~l~g~~i~v~~a~~~  497 (661)
                                            |+|..+     ..+++++|||||+|.+.++|.+|+. +++..++|+.|.|.++.++
T Consensus       124 ----------------------g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          124 ----------------------LEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             ----------------------SEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             ----------------------CeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence                                  667665     5678899999999999999999996 5778899999999999876

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

Probab=99.86  E-value=4.4e-21  Score=185.73  Aligned_cols=182  Identities=14%  Similarity=0.238  Sum_probs=137.8

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcC----C-------CeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQF----G-------NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKIN  251 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~----G-------~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~  251 (661)
                      ..++|||+|||+++++++|+++|++|    |       .|.++.+      +.++|||||+|.+.++|.+|+..++..+.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al~l~g~~~~   76 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAMAFDGIIFQ   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHGGGTTEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHHHhcCCEEc
Confidence            35799999999999999999999999    5       6777776      45689999999999999999955578999


Q ss_pred             CeEEEEEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCC
Q psy15852        252 DKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMV  331 (661)
Q Consensus       252 g~~i~V~~a~~k~~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  331 (661)
                      |+.|.|.++.+..........                                  +                 ....+. 
T Consensus        77 g~~i~v~~~~~~~~~~~~~~~----------------------------------~-----------------~~~~~~-  104 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGMSEN----------------------------------P-----------------SVYVPG-  104 (198)
T ss_dssp             TEEEEEECCCCCCCCCCSSSC----------------------------------S-----------------SCCCTT-
T ss_pred             CceEEEeCCCCCCCCCCCcCC----------------------------------C-----------------cCCCCC-
Confidence            999999998765432100000                                  0                 000000 


Q ss_pred             CCCCCCcccCCCccEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhc
Q psy15852        332 QATPPLAEVDVTGVIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLT  411 (661)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~  411 (661)
                       ...   ..                                           -..-...+++.++.+.+++++|+++|..
T Consensus       105 -~~~---~~-------------------------------------------~~~~~~~l~v~nl~~~~~~~~l~~~f~~  137 (198)
T 2yh0_A          105 -VVS---TV-------------------------------------------VPDSAHKLFIGGLPNYLNDDQVKELLTS  137 (198)
T ss_dssp             -SSC---CC-------------------------------------------SSCCCCEEEEECCCTTCCHHHHHHHHHT
T ss_pred             -Ccc---CC-------------------------------------------CCCCCCEEEEeCCCCCCCHHHHHHHHHH
Confidence             000   00                                           0001123455555556999999999988


Q ss_pred             cCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHh-CCCCcCCCcEEE
Q psy15852        412 KTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK-NPKQKINDKEVD  490 (661)
Q Consensus       412 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~-~~~~~l~g~~i~  490 (661)
                      |                              |.|..+.++.+..+++++|||||+|.+.++|++|+. +++..++|+.|.
T Consensus       138 ~------------------------------G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  187 (198)
T 2yh0_A          138 F------------------------------GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL  187 (198)
T ss_dssp             B------------------------------SCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECE
T ss_pred             c------------------------------CCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            8                              779999999999999999999999999999999996 677889999999


Q ss_pred             EecCCCCCC
Q psy15852        491 VKKATPKPE  499 (661)
Q Consensus       491 v~~a~~~~~  499 (661)
                      |.++.++..
T Consensus       188 v~~a~~~~~  196 (198)
T 2yh0_A          188 VQRASVGAK  196 (198)
T ss_dssp             EEESCCCCC
T ss_pred             EEECCCCCC
Confidence            999987744

>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=99.82  E-value=5.1e-20  Score=171.79  Aligned_cols=132  Identities=14%  Similarity=0.212  Sum_probs=107.2

Q ss_pred             EEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCe-------eecceeehhh-----------hhhccCCeeEe
Q psy15852        128 NVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH-------VINNKKIEAK-----------KAKAKSGKIFV  189 (661)
Q Consensus       128 ~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~-------~i~g~~i~v~-----------~~~~~~~~lfV  189 (661)
                      +++|+.+..  +++|||||+|.++++|++|    +..+++.       .+.+......           ......++|||
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~a----l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v   75 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKV----FKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKV   75 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHH----HHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEE
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHH----HHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEE
Confidence            577888753  6999999999999999998    5444321       1111111110           11123479999


Q ss_pred             cCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCCC
Q psy15852        190 GGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKPE  265 (661)
Q Consensus       190 ~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~~  265 (661)
                      +|||+++++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++.++..
T Consensus        76 ~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A           76 DNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             ESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             eCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            999999999999999999999999999999989999999999999999999999986 6789999999999987653

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

Probab=99.82  E-value=1e-19  Score=176.28  Aligned_cols=175  Identities=15%  Similarity=0.173  Sum_probs=124.1

Q ss_pred             cccccCCCC-CcCccchhhhhhccCcccccCCcccchhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeC
Q psy15852        390 NLLLCDNFP-SIRELEIPEAFLTKTTTVPMTTTEHMVLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFE  468 (661)
Q Consensus       390 ~~~~~~~~p-~~~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~  468 (661)
                      .+++.++.+ .+++++|+++|..|                              |.|..|.++.+.     +|||||+|.
T Consensus         5 ~l~v~nlp~~~~~~~~l~~~F~~~------------------------------G~i~~v~i~~~~-----~g~afV~f~   49 (198)
T 1qm9_A            5 VLLVSNLNPERVTPQSLFILFGVY------------------------------GDVQRVKILFNK-----KENALVQMA   49 (198)
T ss_dssp             EEEEECCCSSSCCHHHHHHHHHTT------------------------------CCCSEEECSTTC-----SSCCEEECT
T ss_pred             EEEEeCCCcccCCHHHHHHHHHhc------------------------------CCEEEEEEEeCC-----CCEEEEEEC
Confidence            466666666 69999999999988                              779999998864     699999999


Q ss_pred             ChHHHHHHHh-CCCCcCCCcEEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccc
Q psy15852        469 HESVVIDLLK-NPKQKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLWQFFD  547 (661)
Q Consensus       469 ~~e~A~~Ai~-~~~~~l~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~~~~~~~~~~~~~~~  547 (661)
                      ++++|++|+. +++..+.|+.|.|.++............... +        ...          .     |.       
T Consensus        50 ~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~-~--------~~~----------~-----~~-------   98 (198)
T 1qm9_A           50 DGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQ-G--------LTK----------D-----YG-------   98 (198)
T ss_dssp             TTHHHHHHHHHHTTCCCSSCCCEEEECCCCSCCCSSSSSSSS-S--------CEE----------E-----SS-------
T ss_pred             CHHHHHHHHHHhCCCeecCeEEEEEEecCCCcCCCCcCCccc-c--------ccc----------c-----cc-------
Confidence            9999999995 7788999999999998865432110000000 0        000          0     00       


Q ss_pred             ccCCCccccccccccCCCCCcccCCCccccccCCCCccccccccCCCeEEEcCCCCCCCHHHHHHHhhcCC-CeeEEEEe
Q psy15852        548 WISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEHFSKYG-EIENVTLK  626 (661)
Q Consensus       548 ~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~te~dL~~~F~~~G-~I~~v~i~  626 (661)
                        .+...       ....|.               ...........++|||+|||+++++++|+++|++|| .|.+|+|+
T Consensus        99 --~~~~~-------r~~~~~---------------~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~  154 (198)
T 1qm9_A           99 --NSPLH-------RFKKPG---------------SKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF  154 (198)
T ss_dssp             --CCCTT-------SSSSCC---------------CCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEES
T ss_pred             --CCchh-------hccCcc---------------ccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEE
Confidence              00000       000000               000011123468999999999999999999999999 99999997


Q ss_pred             ecCCCCCcccEEEEEEcCHHHHHHHHHhCCccc
Q psy15852        627 SDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY  659 (661)
Q Consensus       627 ~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~~  659 (661)
                      .+     ++|+|||+|.+.++|.+|+..+|...
T Consensus       155 ~~-----~~g~afV~f~~~~~A~~A~~~l~g~~  182 (198)
T 1qm9_A          155 QK-----DRKMALIQMGSVEEAVQALIDLHNHD  182 (198)
T ss_dssp             ST-----TSSCEEEECSSHHHHHHHHHHHTSSC
T ss_pred             eC-----CCcEEEEEeCCHHHHHHHHHHhcCCc
Confidence            64     37899999999999999999877543

>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=99.74  E-value=6.5e-18  Score=157.48  Aligned_cols=67  Identities=27%  Similarity=0.347  Sum_probs=63.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|++|+.||+++|||||+|.+.++|.+|++.+|..
T Consensus        69 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~  135 (158)
T 2kn4_A           69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGA  135 (158)
T ss_dssp             BCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            3579999999999999999999999999999999999999999999999999999999999987654

>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=99.73  E-value=3.7e-18  Score=150.05  Aligned_cols=94  Identities=18%  Similarity=0.363  Sum_probs=68.6

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      +|||.+|++++++++|+++|++||+|.+|+|++++  +.+||||||+|.+.++|++|    +..+++..|.|++|.|.++
T Consensus         7 ~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~A----i~~l~~~~~~g~~i~V~~a   80 (115)
T 4f25_A            7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERA----IEKMNGMLLNDRKVFVGRF   80 (115)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHH----HHHHTTCEETTEECEEEES
T ss_pred             EEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHH----HHHcCCCEECCEEEEEEEC
Confidence            45555555599999999999999999999999985  46899999999999999999    8899999999999999887


Q ss_pred             hccC-------------CeeEecCCCccCCHHH
Q psy15852        181 KAKS-------------GKIFVGGLSPEMKDEE  200 (661)
Q Consensus       181 ~~~~-------------~~lfV~nLp~~~te~~  200 (661)
                      .++.             .+|||+|||+++|++.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           81 KSRKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             SCCCC----------------------------
T ss_pred             CCccccccccccccCCCCceEeCCCCCCccccc
Confidence            6543             5799999999999863

>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=99.73  E-value=9.8e-18  Score=155.90  Aligned_cols=97  Identities=23%  Similarity=0.329  Sum_probs=81.4

Q ss_pred             ecceeehhhhhhccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CC
Q psy15852        170 INNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQ  248 (661)
Q Consensus       170 i~g~~i~v~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~  248 (661)
                      +.+............++|||+|||..+++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|.+||+.+ +.
T Consensus        25 ~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~  104 (156)
T 1h2v_Z           25 FRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGT  104 (156)
T ss_dssp             --------CTTTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTS
T ss_pred             cCCChhhhcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            33444444444556789999999999999999999999999999999999999999999999999999999999986 68


Q ss_pred             ccCCeEEEEEeccCCCCC
Q psy15852        249 KINDKEVDVKKATPKPEP  266 (661)
Q Consensus       249 ~~~g~~i~V~~a~~k~~~  266 (661)
                      .|.|+.|.|.++.++...
T Consensus       105 ~~~g~~l~V~~a~~~~~~  122 (156)
T 1h2v_Z          105 RLDDRIIRTDWDAGFKEG  122 (156)
T ss_dssp             EETTEECEEEEESCCCTT
T ss_pred             EECCeEEEEEECCCCCCc
Confidence            999999999999876543

>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=99.72  E-value=6.1e-18  Score=156.19  Aligned_cols=117  Identities=16%  Similarity=0.243  Sum_probs=105.5

Q ss_pred             CCcccEEEEEEeehhhHHHhhHHHHHHh-CCeeecceeehhhhhhc---------------------cCCeeEecCCCcc
Q psy15852        138 GRSRGFAFIVFKDTESLEKASVEDVIAE-GNHVINNKKIEAKKAKA---------------------KSGKIFVGGLSPE  195 (661)
Q Consensus       138 g~srG~afV~F~~~e~A~~A~~~~~~~~-~~~~i~g~~i~v~~~~~---------------------~~~~lfV~nLp~~  195 (661)
                      ...+|+++|+|.+.++|++|    +..+ |+..+.| .+.+.++..                     ..++|||+|||++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a----~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~   84 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKV----FKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNN   84 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTT----HHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSC
T ss_pred             ccccccceeeecCHHHHHHH----HHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCC
Confidence            46899999999999999999    8888 8999999 888877653                     2379999999999


Q ss_pred             CCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCC
Q psy15852        196 MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKP  264 (661)
Q Consensus       196 ~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~  264 (661)
                      +++++|+++|++||.|.+|.++++     ++|||||+|.+.++|.+|+..+ +..+.|++|.|.++.++.
T Consensus        85 ~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           85 GNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             CSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             CCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            999999999999999999999876     5899999999999999999975 788999999999998764

>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=99.72  E-value=7.2e-18  Score=182.20  Aligned_cols=147  Identities=18%  Similarity=0.300  Sum_probs=106.1

Q ss_pred             HHHHHhhcCCCeeEEEEe----eCC-CCCCcccEE--EEEEeehhhHHHhhHHHHHHhCCeeecce--------------
Q psy15852        115 ELKEHFSKYGEIENVTLK----SDP-NTGRSRGFA--FIVFKDTESLEKASVEDVIAEGNHVINNK--------------  173 (661)
Q Consensus       115 ~L~~~F~~~G~I~~v~l~----~~~-~tg~srG~a--fV~F~~~e~A~~A~~~~~~~~~~~~i~g~--------------  173 (661)
                      .|.++|.++|+|..|..+    .++ .+....|++  |+.|....++..+    +..++......+              
T Consensus         8 ~L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~----~~~e~~~~~~~~~~~~k~~~~~~~~~   83 (437)
T 3pgw_S            8 NLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPP----TRAETREERMERKRREKIERRQQEVE   83 (437)
T ss_pred             cHHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCccccccc----ccccCHHHHHHHHHHHHHHHHHHHHH
Confidence            488999999999887333    222 112223333  8888776655443    111110000000              


Q ss_pred             -eeh-------hhhhhccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHh
Q psy15852        174 -KIE-------AKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN  245 (661)
Q Consensus       174 -~i~-------v~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~  245 (661)
                       .+.       ........++|||+|||+.+++++|+++|++||.|..|.|+.+..+++++|||||+|.+.++|.+||+.
T Consensus        84 ~~~~~~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~  163 (437)
T 3pgw_S           84 TELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH  163 (437)
T ss_pred             HhhhhcCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHH
Confidence             000       001112237999999999999999999999999999999999988999999999999999999999988


Q ss_pred             C-CCccCCeEEEEEeccCCCC
Q psy15852        246 P-KQKINDKEVDVKKATPKPE  265 (661)
Q Consensus       246 ~-~~~~~g~~i~V~~a~~k~~  265 (661)
                      + +..|.|+.|.|.++.++..
T Consensus       164 lng~~i~gr~i~V~~a~~~~~  184 (437)
T 3pgw_S          164 ADGKKIDGRRVLVDVERGRTV  184 (437)
T ss_pred             cCCCEECCEEEEEEEeCCCCC
Confidence            6 6899999999999987654

>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=99.70  E-value=3.6e-17  Score=139.49  Aligned_cols=79  Identities=16%  Similarity=0.349  Sum_probs=75.3

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      .++|||+|||+++|+++|+++|++||+|.+|++++++.+|.++|||||+|.+.++|.+|++.+ +..+.|++|.|.+|+|
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            478999999999999999999999999999999999999999999999999999999999875 7899999999999975

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.69  E-value=3.4e-17  Score=137.36  Aligned_cols=82  Identities=20%  Similarity=0.387  Sum_probs=76.4

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCC-CeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-C-CccCCeEEEEEecc
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFG-NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-K-QKINDKEVDVKKAT  261 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G-~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~-~~~~g~~i~V~~a~  261 (661)
                      ++|||+|||+++|+++|+++|++|| +|.+|+|++++.++.++|||||+|.+.++|.+|++.+ + ..++|++|.|.++.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            6899999999999999999999999 8999999999999999999999999999999999986 3 47999999999999


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      +++..
T Consensus        82 ~~~~~   86 (91)
T 2lxi_A           82 PKPKI   86 (91)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87653

>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=99.67  E-value=1e-16  Score=136.64  Aligned_cols=79  Identities=23%  Similarity=0.362  Sum_probs=72.6

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+.|||+|+| ++|+++|+++|++||+|.+|+|++++.+|+++|||||+|.++++|++|    +..+|+..+.|++|.|.
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~A----i~~lng~~~~gr~l~V~   94 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA----INTLNGLRLQSKTIKVS   94 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHH----HHHhCCCEECCEEEEEE
Confidence            4455666555 999999999999999999999999999999999999999999999999    88999999999999999


Q ss_pred             hhhc
Q psy15852        179 KAKA  182 (661)
Q Consensus       179 ~~~~  182 (661)
                      +++|
T Consensus        95 ~AkP   98 (99)
T 4fxv_A           95 YARP   98 (99)
T ss_dssp             ECCB
T ss_pred             EeeC
Confidence            9876

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

Probab=99.66  E-value=6.7e-16  Score=135.80  Aligned_cols=85  Identities=26%  Similarity=0.462  Sum_probs=79.2

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      ...++|||+|||+++++++|+++|++||.|..|.|++++.+++++|||||+|.+.++|++||+.++..+.|+.|.|.++.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~   94 (116)
T 2cqd_A           15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAY   94 (116)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEEST
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEEEEEcc
Confidence            34589999999999999999999999999999999999999999999999999999999999998779999999999998


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++..+
T Consensus        95 ~~~~~   99 (116)
T 2cqd_A           95 LGAKP   99 (116)
T ss_dssp             TTCCC
T ss_pred             cCCCc
Confidence            76544

>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=99.65  E-value=1e-15  Score=130.57  Aligned_cols=84  Identities=26%  Similarity=0.431  Sum_probs=78.6

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||+++++++|+++|++||+|..|.++.++.++.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   86 (99)
T 1whw_A            7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            4579999999999999999999999999999999999988999999999999999999999776 678999999999999


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++...
T Consensus        87 ~~~~~   91 (99)
T 1whw_A           87 IKKEA   91 (99)
T ss_dssp             CCSTT
T ss_pred             CCccc
Confidence            87654

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

Probab=99.64  E-value=1.1e-15  Score=130.46  Aligned_cols=85  Identities=38%  Similarity=0.610  Sum_probs=79.3

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      ...++|||+|||.++++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+|++..+..++|+.|.|.++.
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a~   87 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAE   87 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            34589999999999999999999999999999999999999999999999999999999999966789999999999999


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++...
T Consensus        88 ~~~~~   92 (99)
T 2dgs_A           88 PRDSK   92 (99)
T ss_dssp             CCCCC
T ss_pred             CCccc
Confidence            87654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.64  E-value=1.3e-16  Score=134.43  Aligned_cols=79  Identities=19%  Similarity=0.325  Sum_probs=72.7

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCC--eEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-C----CccCCeEEE
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGN--IIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-K----QKINDKEVD  256 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~--i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~----~~~~g~~i~  256 (661)
                      -.+|||+|||+++|+++|+++|++||.  |.+|++++|+.+++++|||||+|.+.++|++|++.+ +    ..++||+|.
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~   88 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIG   88 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEE
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEE
Confidence            368999999999999999999999995  679999999999999999999999999999999986 3    259999999


Q ss_pred             EEeccC
Q psy15852        257 VKKATP  262 (661)
Q Consensus       257 V~~a~~  262 (661)
                      |.+|++
T Consensus        89 V~~Aks   94 (95)
T 2lkz_A           89 VDFAKS   94 (95)
T ss_dssp             EEECCC
T ss_pred             EEEccC
Confidence            999875

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

Probab=99.64  E-value=8.4e-16  Score=129.95  Aligned_cols=84  Identities=20%  Similarity=0.380  Sum_probs=78.5

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +..++|||+|||.++++++|+++|++||.|..|.+++++.+++++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++
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            35689999999999999999999999999999999999999999999999999999999999965 78999999999999


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .++..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            88764

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

Probab=99.64  E-value=5.1e-16  Score=134.91  Aligned_cols=83  Identities=10%  Similarity=0.152  Sum_probs=77.6

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +..++|||+|||+++++++|+++|++||.|.+|.|++++.|++++|||||+|.+.++|++|++.+ +..+.|+.|.|.++
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            45679999999999999999999999999999999999999999999999999999999999976 68999999999999


Q ss_pred             cCCC
Q psy15852        261 TPKP  264 (661)
Q Consensus       261 ~~k~  264 (661)
                      ....
T Consensus        84 ~~~~   87 (110)
T 3s8s_A           84 IKGQ   87 (110)
T ss_dssp             STTH
T ss_pred             CCCc
Confidence            7654

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

Probab=99.63  E-value=9.4e-16  Score=129.93  Aligned_cols=84  Identities=25%  Similarity=0.426  Sum_probs=78.4

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEE-EeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIET-EMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v-~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ..++|||+|||.++++++|+++|++||.|..| .|++++.++.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45799999999999999999999999999999 99999889999999999999999999999976 68899999999999


Q ss_pred             cCCCCC
Q psy15852        261 TPKPEP  266 (661)
Q Consensus       261 ~~k~~~  266 (661)
                      .++..+
T Consensus        84 ~~~~~~   89 (96)
T 1x5t_A           84 FKKDSK   89 (96)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            887643

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

Probab=99.63  E-value=3e-16  Score=141.81  Aligned_cols=119  Identities=11%  Similarity=0.152  Sum_probs=78.7

Q ss_pred             EEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh----hhhhccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEecc
Q psy15852        143 FAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA----KKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPY  218 (661)
Q Consensus       143 ~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v----~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~  218 (661)
                      +.|++|.+...|..|    +..+++....|+...-    .......++|||+|||+++++++|+++|++||.|..|.|+.
T Consensus         6 ~~~~~~~~~~~~~~a----~~~~~g~~~~g~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~   81 (135)
T 2lea_A            6 HHHHHSSGLVPRGSH----MASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR   81 (135)
T ss_dssp             ---------------------------------CCSCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCC
T ss_pred             cccccccCCCchhhh----hhhccCCCCCCCCCCCcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEe
Confidence            567777777778887    7777665554433211    11122347899999999999999999999999999999999


Q ss_pred             CCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCCC
Q psy15852        219 DKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKPE  265 (661)
Q Consensus       219 ~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~~  265 (661)
                      ++.+++++|||||+|.+.++|++|++.+ +..+.|+.|.|.++.++..
T Consensus        82 ~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~  129 (135)
T 2lea_A           82 DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  129 (135)
T ss_dssp             CSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCC
T ss_pred             cCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            9888999999999999999999999986 6889999999999987654

>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=99.62  E-value=1e-15  Score=127.24  Aligned_cols=79  Identities=29%  Similarity=0.630  Sum_probs=75.1

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+++++++|+++|++||.|..|.+++++.+++++|||||+|.+.++|.+|++.++..++|+.|.|++|
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            4568999999999999999999999999999999999999999999999999999999999998888999999999875

>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=6.8e-16  Score=137.92  Aligned_cols=84  Identities=19%  Similarity=0.369  Sum_probs=78.2

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|++.+ +..|+|+.|.|.++.
T Consensus        21 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  100 (126)
T 3ex7_B           21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF  100 (126)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEec
Confidence            3579999999999999999999999999999999999989999999999999999999999875 789999999999998


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++..+
T Consensus       101 ~~~~~  105 (126)
T 3ex7_B          101 VRGPP  105 (126)
T ss_dssp             ESSSC
T ss_pred             CCCCC
Confidence            87654

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

Probab=99.62  E-value=1.1e-15  Score=138.93  Aligned_cols=84  Identities=15%  Similarity=0.305  Sum_probs=78.3

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||.++++++|+++|++||+|.+|.|++++.+++++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++.
T Consensus        41 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  120 (139)
T 1u6f_A           41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            3489999999999999999999999999999999999989999999999999999999999986 678999999999999


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++..+
T Consensus       121 ~~~~~  125 (139)
T 1u6f_A          121 SGHQR  125 (139)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87644

>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=1.7e-15  Score=133.20  Aligned_cols=83  Identities=25%  Similarity=0.471  Sum_probs=78.5

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK  263 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k  263 (661)
                      .++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||+.++..|+|+.|.|.++.++
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~~  106 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAR  106 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECCCC
Confidence            37999999999999999999999999999999999999999999999999999999999999778999999999999987


Q ss_pred             CCC
Q psy15852        264 PEP  266 (661)
Q Consensus       264 ~~~  266 (661)
                      ...
T Consensus       107 ~~~  109 (116)
T 1x4b_A          107 EES  109 (116)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            653

>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=99.61  E-value=2.5e-16  Score=142.31  Aligned_cols=123  Identities=7%  Similarity=0.132  Sum_probs=74.0

Q ss_pred             ccEEEEEEeehhhHHHhhHHHHHHhCCeeeccee--ehhhhhhccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEecc
Q psy15852        141 RGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK--IEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPY  218 (661)
Q Consensus       141 rG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~--i~v~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~  218 (661)
                      +|+||.+|..++.+..|..+......+.......  -.........++|||+|||+++++++|+++|++|| |.+|.|++
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~gg~~~g~~~g~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~   79 (139)
T 2hgn_A            1 MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEI   79 (139)
T ss_dssp             --------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCC
T ss_pred             CCcccccccCccccchhcccchhccCCCCCCCCCCCcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEE
Confidence            3678888888888777622211111111111000  01112233457999999999999999999999999 67999999


Q ss_pred             CCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCCCC
Q psy15852        219 DKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE  265 (661)
Q Consensus       219 ~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k~~  265 (661)
                      ++. ++++|||||+|.+.++|++||+.++..|+|+.|.|.++.++..
T Consensus        80 d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           80 GPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             SSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECCCSCC
T ss_pred             CCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECCCCCC
Confidence            986 9999999999999999999996557899999999999887653

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

Probab=99.61  E-value=1.5e-15  Score=130.58  Aligned_cols=85  Identities=22%  Similarity=0.370  Sum_probs=79.0

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||.++++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (103)
T 2cq0_A           13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   92 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEC
Confidence            44589999999999999999999999999999999999888999999999999999999999976 68999999999999


Q ss_pred             cCCCCC
Q psy15852        261 TPKPEP  266 (661)
Q Consensus       261 ~~k~~~  266 (661)
                      .++...
T Consensus        93 ~~~~~~   98 (103)
T 2cq0_A           93 KPSTNS   98 (103)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            987643

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

Probab=99.61  E-value=2.3e-15  Score=130.76  Aligned_cols=84  Identities=29%  Similarity=0.508  Sum_probs=78.0

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      ...++|||+|||.++++++|+++|++||.|.+|.+++++.++.++|||||+|.+.++|.+|++.++..++|+.|.|.++.
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~a~  102 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAF  102 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEcc
Confidence            34589999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy15852        262 PKPE  265 (661)
Q Consensus       262 ~k~~  265 (661)
                      ++..
T Consensus       103 ~~~~  106 (109)
T 2rs2_A          103 PRRA  106 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>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=99.61  E-value=1.2e-15  Score=126.62  Aligned_cols=81  Identities=27%  Similarity=0.434  Sum_probs=74.7

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||.++++++|+++|++||.|.+|.++.++.++.++|||||+|.+.++|.+|++.+ +..++|+.|.|.++.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            4578999999999999999999999999999999999888999999999999999999999975 789999999999998


Q ss_pred             CC
Q psy15852        262 PK  263 (661)
Q Consensus       262 ~k  263 (661)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            75

>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=99.61  E-value=9e-16  Score=141.58  Aligned_cols=123  Identities=16%  Similarity=0.067  Sum_probs=92.5

Q ss_pred             CCcccceEEEEeCChHHHHHHHhC--CCCcCCCcEEEEecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy15852        456 KSQRKNFCFITFEHESVVIDLLKN--PKQKINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG  533 (661)
Q Consensus       456 ~~~~~g~aFV~F~~~e~A~~Ai~~--~~~~l~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~gg~~~~g~~  533 (661)
                      ..+.+|+++|+|.+.++|++|+..  ++..++| .+.+..+..........                             
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~-----------------------------   58 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGS-----------------------------   58 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSS-----------------------------
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccccc-----------------------------
Confidence            346689999999999999999944  4578899 99998776432110000                             


Q ss_pred             CCCCCCccccccccccCCCccccccccccCCCCCcccCCCccccccCCCCccccccccCCCeEEEcCCCCCCCHHHHHHH
Q psy15852        534 YGELDYLQLWQFFDWISSSFSENCLLEDSIGKPLTVSCSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEELKEH  613 (661)
Q Consensus       534 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~te~dL~~~  613 (661)
                                                     .+.              ............++|||+|||+++|+++|+++
T Consensus        59 -------------------------------~~~--------------~~~~~~~~~~~~~~l~V~nl~~~~t~~~l~~~   93 (150)
T 2i2y_A           59 -------------------------------HHH--------------HHHMHRDSCPLDCKVYVGNLGNNGNKTELERA   93 (150)
T ss_dssp             -------------------------------SSC--------------CCCSCSSSSTTSCEEEEESCCSCCSCHHHHHH
T ss_pred             -------------------------------ccc--------------cccccccCCCCCCEEEEeCCCCCCCHHHHHHH
Confidence                                           000              00000011223689999999999999999999


Q ss_pred             hhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        614 FSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       614 F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      |++||.|.+|+|+++     ++|||||+|.+.++|.+|+..+|..
T Consensus        94 F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~  133 (150)
T 2i2y_A           94 FGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGR  133 (150)
T ss_dssp             HHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSS
T ss_pred             HHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCC
Confidence            999999999999986     6899999999999999999976653

>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=99.61  E-value=2.7e-15  Score=129.37  Aligned_cols=85  Identities=25%  Similarity=0.410  Sum_probs=79.1

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   92 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   92 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            34589999999999999999999999999999999999989999999999999999999999986 68999999999999


Q ss_pred             cCCCCC
Q psy15852        261 TPKPEP  266 (661)
Q Consensus       261 ~~k~~~  266 (661)
                      .++...
T Consensus        93 ~~~~~~   98 (105)
T 1x5u_A           93 SAHNKN   98 (105)
T ss_dssp             TTTSCC
T ss_pred             CCCCcC
Confidence            887653

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

Probab=99.61  E-value=1.5e-15  Score=130.33  Aligned_cols=85  Identities=25%  Similarity=0.517  Sum_probs=78.8

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +..++|||+|||+++++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|++.+ +..++|+.|.|.++
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   89 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   89 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34689999999999999999999999999999999999989999999999999999999999775 68899999999999


Q ss_pred             cCCCCC
Q psy15852        261 TPKPEP  266 (661)
Q Consensus       261 ~~k~~~  266 (661)
                      .++...
T Consensus        90 ~~~~~~   95 (102)
T 1x5s_A           90 GKSSDN   95 (102)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            987653

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

Probab=99.61  E-value=1.7e-15  Score=129.88  Aligned_cols=85  Identities=25%  Similarity=0.509  Sum_probs=78.8

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|.+|++.+ +..++|+.|.|.++
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            34589999999999999999999999999999999999889999999999999999999999875 68899999999999


Q ss_pred             cCCCCC
Q psy15852        261 TPKPEP  266 (661)
Q Consensus       261 ~~k~~~  266 (661)
                      .++...
T Consensus        90 ~~~~~~   95 (102)
T 2cqb_A           90 KPMRIK   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            887654

>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=99.61  E-value=1.9e-15  Score=124.25  Aligned_cols=80  Identities=18%  Similarity=0.395  Sum_probs=75.8

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      .+|||+|||+++++++|+++|++||+|.++.+++++.++.++|||||+|.+.++|.+|++.+ +..++|+.|.|.++.++
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            47999999999999999999999999999999999889999999999999999999999975 78999999999999876


Q ss_pred             C
Q psy15852        264 P  264 (661)
Q Consensus       264 ~  264 (661)
                      +
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.61  E-value=1.6e-15  Score=131.82  Aligned_cols=81  Identities=21%  Similarity=0.207  Sum_probs=73.3

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      +.++++|.+|++++++++|+++|++||+|.+|+|++|+.|+++||||||+|.+.++|++|    +..+|+..+.|+.|.|
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~A----i~~lng~~~~gr~i~V   80 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKET----VKNLHLTSVMGNIIHA   80 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH----HHHHTTCEETTEECEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHH----HHHhCCCEECCeEEEE
Confidence            345566666666999999999999999999999999999999999999999999999999    9999999999999999


Q ss_pred             hhhhc
Q psy15852        178 KKAKA  182 (661)
Q Consensus       178 ~~~~~  182 (661)
                      .++..
T Consensus        81 ~~a~~   85 (110)
T 3s8s_A           81 QLDIK   85 (110)
T ss_dssp             EECST
T ss_pred             EECCC
Confidence            87754

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.60  E-value=2.9e-16  Score=131.70  Aligned_cols=81  Identities=20%  Similarity=0.315  Sum_probs=72.0

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCC-CeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHh-CCeeecceeehh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYG-EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE-GNHVINNKKIEA  177 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G-~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~-~~~~i~g~~i~v  177 (661)
                      +++++.+|++++||++|+++|++|| +|.+|+|++++.||++||||||+|.++++|++|    +..+ ++..+.|++|.|
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~A----i~~~~~~~~~~gr~i~V   77 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRW----MEANQHSLNILGQKVSM   77 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHH----HHTTTTEEEETTEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHH----HHhcCCCeEECCEEEEE
Confidence            4566666666999999999999999 799999999999999999999999999999998    7665 567899999999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .++.++.
T Consensus        78 ~~a~~~~   84 (91)
T 2lxi_A           78 HYSDPKP   84 (91)
T ss_dssp             ECCCSCC
T ss_pred             EEcCCCC
Confidence            9988764

>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=99.60  E-value=3.5e-16  Score=154.46  Aligned_cols=81  Identities=19%  Similarity=0.332  Sum_probs=75.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCC--CeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFG--NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G--~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                      ..++|||+|||+++++++|+++|++||  .|.+|+|++++.+++++|||||+|.+.++|.+||+.+ +..|.|+.|.|.+
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            457899999999999999999999999  9999999999999999999999999999999999987 6899999999999


Q ss_pred             ccCC
Q psy15852        260 ATPK  263 (661)
Q Consensus       260 a~~k  263 (661)
                      +.++
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8653

>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=99.60  E-value=4.1e-15  Score=130.65  Aligned_cols=84  Identities=30%  Similarity=0.512  Sum_probs=77.6

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||.++++++|+++|++||.|..|.|+.+. ++.++|||||+|.+.++|++|++.+ +..++|+.|.|.++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            345799999999999999999999999999999999988 8999999999999999999999986 68999999999999


Q ss_pred             cCCCCC
Q psy15852        261 TPKPEP  266 (661)
Q Consensus       261 ~~k~~~  266 (661)
                      .++...
T Consensus        84 ~~~~~~   89 (116)
T 2fy1_A           84 KKPSFQ   89 (116)
T ss_dssp             CCSSCS
T ss_pred             CCCCCC
Confidence            876643

>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=99.60  E-value=3.5e-15  Score=128.19  Aligned_cols=85  Identities=20%  Similarity=0.407  Sum_probs=78.9

Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||+. ++.++|+.|.|.++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~l~v~~a   90 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMIDGRWCDCKLP   90 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS-CEEETTEEEEEECC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc-CCeeCCeEEEEEec
Confidence            34568999999999999999999999999999999999998999999999999999999999995 67899999999999


Q ss_pred             cCCCCC
Q psy15852        261 TPKPEP  266 (661)
Q Consensus       261 ~~k~~~  266 (661)
                      .++...
T Consensus        91 ~~~~~~   96 (103)
T 2cqg_A           91 NSKQSQ   96 (103)
T ss_dssp             CTTCCC
T ss_pred             CCCCcC
Confidence            987654

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

Probab=99.60  E-value=7e-15  Score=129.03  Aligned_cols=85  Identities=29%  Similarity=0.489  Sum_probs=79.0

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||..+++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|++|++.+ +..|.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   92 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34579999999999999999999999999999999999888999999999999999999999986 68999999999999


Q ss_pred             cCCCCC
Q psy15852        261 TPKPEP  266 (661)
Q Consensus       261 ~~k~~~  266 (661)
                      .++...
T Consensus        93 ~~~~~~   98 (115)
T 2dgo_A           93 TRKPPA   98 (115)
T ss_dssp             SCCCCC
T ss_pred             cCCCCC
Confidence            987654

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

Probab=99.60  E-value=2.2e-15  Score=129.42  Aligned_cols=84  Identities=14%  Similarity=0.267  Sum_probs=78.1

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.+ +..++|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA   90 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEC
Confidence            34589999999999999999999999999999999999999999999999999999999999975 78999999999999


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .++..
T Consensus        91 ~~~~~   95 (103)
T 2dnm_A           91 RYGRR   95 (103)
T ss_dssp             SSCCS
T ss_pred             CcCCC
Confidence            87654

>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=99.60  E-value=4.3e-15  Score=129.50  Aligned_cols=85  Identities=18%  Similarity=0.332  Sum_probs=78.9

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-------CCccCCeE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-------KQKINDKE  254 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-------~~~~~g~~  254 (661)
                      ...++|||+|||+++++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+|++.+       +..++|+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~   92 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   92 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEE
Confidence            34589999999999999999999999999999999999999999999999999999999999976       57899999


Q ss_pred             EEEEeccCCCCC
Q psy15852        255 VDVKKATPKPEP  266 (661)
Q Consensus       255 i~V~~a~~k~~~  266 (661)
                      |.|.++.++...
T Consensus        93 l~v~~a~~~~~~  104 (111)
T 1x4h_A           93 LKVDLAVTRDEA  104 (111)
T ss_dssp             EEEECCCCCCCC
T ss_pred             EEEEECCCCccC
Confidence            999999987654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=1.5e-15  Score=131.07  Aligned_cols=85  Identities=27%  Similarity=0.562  Sum_probs=79.5

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      ...++|||+|||+.+++++|+++|++||+|..|.|++++.++.++|||||+|.+.++|++||+..+..|+|+.|.|.++.
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~a~   93 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCT   93 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCCSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEcc
Confidence            44589999999999999999999999999999999999989999999999999999999999997789999999999999


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++...
T Consensus        94 ~~~~~   98 (105)
T 2dh8_A           94 PRGMQ   98 (105)
T ss_dssp             CSSCC
T ss_pred             CCCCC
Confidence            87654

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

Probab=99.60  E-value=2.8e-15  Score=127.55  Aligned_cols=85  Identities=18%  Similarity=0.351  Sum_probs=77.5

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCC---CCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKS---KSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDV  257 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~---~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V  257 (661)
                      +..++|||+|||+++++++|+++|++||.|..|.++.++.   ++.++|||||+|.+.++|.+|++.+ +..++|+.|.|
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            3457999999999999999999999999999999998876   6689999999999999999999986 68999999999


Q ss_pred             EeccCCCCC
Q psy15852        258 KKATPKPEP  266 (661)
Q Consensus       258 ~~a~~k~~~  266 (661)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999887643

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

Probab=99.59  E-value=4.5e-15  Score=128.40  Aligned_cols=85  Identities=15%  Similarity=0.318  Sum_probs=78.7

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccC-CCCCCcCcEEEEEeCCHHHHHHHHHhC--CCccCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYD-KSKSQRKNFCFITFEHESVVIDLLKNP--KQKINDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~-~~~g~~~g~afV~f~~~~~A~~Al~~~--~~~~~g~~i~V~  258 (661)
                      ...++|||+|||..+++++|+++|++||.|..|.|+++ +.++.++|||||+|.+.++|.+|++.+  +..+.|+.|.|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~   92 (107)
T 2cph_A           13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   92 (107)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEE
Confidence            34589999999999999999999999999999999998 778999999999999999999999986  689999999999


Q ss_pred             eccCCCCC
Q psy15852        259 KATPKPEP  266 (661)
Q Consensus       259 ~a~~k~~~  266 (661)
                      ++.++...
T Consensus        93 ~a~~~~~~  100 (107)
T 2cph_A           93 WADSEVTV  100 (107)
T ss_dssp             ECCCCCCC
T ss_pred             eCCCCCCC
Confidence            99987654

>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=99.59  E-value=3.9e-15  Score=126.11  Aligned_cols=82  Identities=16%  Similarity=0.328  Sum_probs=77.1

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      +++|||+|||..+++++|+++|++||.|.+|.++.++.++.++|||||+|.+.++|.+|++.+ +..++|+.|.|.++.+
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            478999999999999999999999999999999999989999999999999999999999875 7899999999999988


Q ss_pred             CCC
Q psy15852        263 KPE  265 (661)
Q Consensus       263 k~~  265 (661)
                      +..
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            654

>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=99.59  E-value=5.2e-15  Score=127.34  Aligned_cols=84  Identities=21%  Similarity=0.399  Sum_probs=76.8

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCC-CCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSK-SQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~-g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+++++++|+++|++|| |..|.|++++.+ ++++|||||+|.+.++|.+||...+..+.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   91 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEEEc
Confidence            3458999999999999999999999999 999999999988 99999999999999999999944478999999999999


Q ss_pred             cCCCCC
Q psy15852        261 TPKPEP  266 (661)
Q Consensus       261 ~~k~~~  266 (661)
                      .++...
T Consensus        92 ~~~~~~   97 (104)
T 1wi8_A           92 DQAQDK   97 (104)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            987643

>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=99.59  E-value=2.8e-15  Score=131.57  Aligned_cols=84  Identities=20%  Similarity=0.399  Sum_probs=78.3

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||.++++++|+++|++||.|.+|.|++++.+++++|||||+|.+.++|++|++.+ +..|.|+.|.|.++.
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  103 (115)
T 2cpz_A           24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR  103 (115)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            4589999999999999999999999999999999999988999999999999999999999875 789999999999998


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++...
T Consensus       104 ~~~~~  108 (115)
T 2cpz_A          104 SKNDS  108 (115)
T ss_dssp             CSCCC
T ss_pred             CCCcC
Confidence            87653

>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=99.59  E-value=3.1e-15  Score=123.62  Aligned_cols=80  Identities=25%  Similarity=0.533  Sum_probs=74.9

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +..++|||+|||+++++++|+++|++||.|..|.+++++.++.++|||||+|.+.++|.+|++.+ +..++|++|.|.++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            35689999999999999999999999999999999999889999999999999999999999775 78999999999997


Q ss_pred             c
Q psy15852        261 T  261 (661)
Q Consensus       261 ~  261 (661)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.59  E-value=5.4e-15  Score=127.03  Aligned_cols=83  Identities=20%  Similarity=0.372  Sum_probs=76.5

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      ...++|||+|||+++++++|+++|++|| |..|.|++++.+++++|||||+|.+.++|.+|++.++..+.|+.|.|.++.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~   91 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAE   91 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEECC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEEec
Confidence            3458999999999999999999999997 999999999999999999999999999999999545789999999999998


Q ss_pred             CCCC
Q psy15852        262 PKPE  265 (661)
Q Consensus       262 ~k~~  265 (661)
                      ++..
T Consensus        92 ~~~~   95 (103)
T 2dng_A           92 GRKQ   95 (103)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8654

>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=99.58  E-value=2.5e-15  Score=131.83  Aligned_cols=81  Identities=25%  Similarity=0.480  Sum_probs=73.6

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      ..+|||+|||+++++++|+++|++||.|.+|+|+++.  +.++|||||+|.+.++|++||+.+ +..++|+.|.|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999886  457999999999999999999875 7899999999999987


Q ss_pred             CCCC
Q psy15852        263 KPEP  266 (661)
Q Consensus       263 k~~~  266 (661)
                      +..+
T Consensus        83 ~~~~   86 (115)
T 4f25_A           83 RKER   86 (115)
T ss_dssp             CCC-
T ss_pred             cccc
Confidence            6543

>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=99.58  E-value=1.3e-15  Score=133.70  Aligned_cols=102  Identities=20%  Similarity=0.282  Sum_probs=89.4

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+++++.++++++++++|+++|++||+|.+|+|+++   +.++|||||+|.+.++|.+|    +..+++..+.|+.|.|.
T Consensus         8 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l~v~   80 (115)
T 3lqv_A            8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNA----VDHLSGFNVSNRYLVVL   80 (115)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHH----HHHHTTCBSSSCBCEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHH----HHHcCCCEECCeEEEEE
Confidence            445555555559999999999999999999999976   55799999999999999999    88899999999999999


Q ss_pred             hhhccCCeeEecCCCccCCHHHHHHHHhcCCC
Q psy15852        179 KAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGN  210 (661)
Q Consensus       179 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~  210 (661)
                      ++.++...   ++++...++++|+++|++||-
T Consensus        81 ~a~~~~~~---~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           81 YYNANRAF---QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             ECCHHHHT---TTSCHHHHHHHHHHHHHHHCC
T ss_pred             EecCChhh---hhhhHhHhHHHHHHHHHHhCC
Confidence            98765433   789999999999999999983

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

Probab=99.58  E-value=1.7e-15  Score=121.94  Aligned_cols=75  Identities=40%  Similarity=0.655  Sum_probs=71.4

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      +|||+|||+++++++|+++|++||+|.+|.++.++.+++++|||||+|.+.++|++|++..+..++|++|.|++|
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 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            589999999999999999999999999999999998899999999999999999999986688999999999875

>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=99.58  E-value=4e-15  Score=123.54  Aligned_cols=66  Identities=44%  Similarity=0.656  Sum_probs=62.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|++++.||+++|||||+|.+.++|.+|++.+++
T Consensus        10 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~   75 (87)
T 3s7r_A           10 DAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEH   75 (87)
T ss_dssp             CTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCC
Confidence            468999999999999999999999999999999999999999999999999999999999987443

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

Probab=99.58  E-value=5.4e-15  Score=124.70  Aligned_cols=80  Identities=14%  Similarity=0.344  Sum_probs=75.1

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +..++|||+|||+.+++++|+++|++||+|..|.++.++.++.++|||||+|.+.++|.+|++.+ +..+.|++|.|.++
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            44589999999999999999999999999999999999999999999999999999999999876 67899999999997


Q ss_pred             c
Q psy15852        261 T  261 (661)
Q Consensus       261 ~  261 (661)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.58  E-value=8.2e-16  Score=129.61  Aligned_cols=81  Identities=21%  Similarity=0.340  Sum_probs=72.5

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCC--eeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCe----eec
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGE--IENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH----VIN  171 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~--I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~----~i~  171 (661)
                      .-+++|+.+|++++|+++|+++|++||.  |.+|+|++|+.||++||||||+|.++++|++|    +..+|+.    .|.
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~A----i~~lng~~~~~~i~   83 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL----LQILQSLHPPLKID   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHH----HHHHHSSSSCEEET
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHH----HHHhcCCCCCceEC
Confidence            3467777778789999999999999995  77999999999999999999999999999999    8888875    699


Q ss_pred             ceeehhhhhhc
Q psy15852        172 NKKIEAKKAKA  182 (661)
Q Consensus       172 g~~i~v~~~~~  182 (661)
                      |++|.|.+++.
T Consensus        84 Gr~i~V~~Aks   94 (95)
T 2lkz_A           84 GKTIGVDFAKS   94 (95)
T ss_dssp             TEEEEEEECCC
T ss_pred             CEEEEEEEccC
Confidence            99999998864

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

Probab=99.58  E-value=2.9e-15  Score=128.41  Aligned_cols=79  Identities=15%  Similarity=0.320  Sum_probs=74.2

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      ..++|||+|||+++|+++|+++|++||+|.+|.|++++. +.++|||||+|.+.++|.+|+..+++.++|+.|.|.++..
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEchH
Confidence            457999999999999999999999999999999999987 9999999999999999999999667899999999998765

>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=99.58  E-value=2.5e-15  Score=140.87  Aligned_cols=82  Identities=17%  Similarity=0.337  Sum_probs=76.2

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||+.+ +..|.|+.|.|.|+.++
T Consensus        73 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  152 (165)
T 1rk8_A           73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK  152 (165)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            67999999999999999999999999999999999989999999999999999999999975 68899999999999887


Q ss_pred             CCC
Q psy15852        264 PEP  266 (661)
Q Consensus       264 ~~~  266 (661)
                      ...
T Consensus       153 ~~~  155 (165)
T 1rk8_A          153 GPK  155 (165)
T ss_dssp             C--
T ss_pred             CCC
Confidence            643

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

Probab=99.58  E-value=1e-15  Score=130.82  Aligned_cols=81  Identities=15%  Similarity=0.292  Sum_probs=76.1

Q ss_pred             CCeeEecCCCc------cCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC-eEE
Q psy15852        184 SGKIFVGGLSP------EMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND-KEV  255 (661)
Q Consensus       184 ~~~lfV~nLp~------~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g-~~i  255 (661)
                      .++|||+|||.      ++++++|+++|++||.|.+|.|++++.|++++|||||+|.+.++|.+|++.+ +..+.| +.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            46899999999      9999999999999999999999999999999999999999999999999875 789999 999


Q ss_pred             EEEeccCCC
Q psy15852        256 DVKKATPKP  264 (661)
Q Consensus       256 ~V~~a~~k~  264 (661)
                      .|.++.++.
T Consensus        86 ~V~~a~~~~   94 (100)
T 3ns6_A           86 FLYTMKDVE   94 (100)
T ss_dssp             EEEESHHHH
T ss_pred             EEEECchhh
Confidence            999998653

>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=99.58  E-value=8.3e-16  Score=128.65  Aligned_cols=82  Identities=17%  Similarity=0.301  Sum_probs=70.7

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCC--CeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFG--NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G--~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      .+|||+|||+++++++|+++|++||  .|.+|.++.++.+|+++|||||+|.+.++|.+|++.+ +..++|+.|.|.++.
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  9999999999999999999999999999999999876 689999999999998


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++..+
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            86543

>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=122.95  Aligned_cols=76  Identities=30%  Similarity=0.523  Sum_probs=73.3

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      ++|||+|||+++++++|+++|++||+|..|.+++++.+++++|||||+|.+.++|.+|++.++..++|++|.|++|
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 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCccCCEEEEEEec
Confidence            4799999999999999999999999999999999998999999999999999999999999889999999999987

>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=99.58  E-value=5.8e-15  Score=123.11  Aligned_cols=80  Identities=23%  Similarity=0.382  Sum_probs=75.0

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK  263 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k  263 (661)
                      .++|||+|||+++++++|+++|++||.|.+|.++.++.+++++|||||+|.+.++|.+|+..++..+.|+.|.|.++.++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccCC
Confidence            47899999999999999999999999999999999988999999999999999999999944578999999999999764

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

Probab=99.58  E-value=5.7e-15  Score=126.10  Aligned_cols=83  Identities=17%  Similarity=0.348  Sum_probs=76.8

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||..+++++|+++|++||.|..|.++.++ +++++|||||+|.+.++|.+|++.+ +..++|+.|.|.++
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            345899999999999999999999999999999999988 7999999999999999999999875 68899999999999


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .++..
T Consensus        94 ~~~~~   98 (100)
T 2do4_A           94 NSGPS   98 (100)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            88754

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

Probab=99.58  E-value=4.5e-15  Score=127.71  Aligned_cols=84  Identities=21%  Similarity=0.357  Sum_probs=77.3

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhc-CCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCc-cCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQ-FGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQK-INDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~-~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~-~~g~~i~V~  258 (661)
                      ...++|||+|||+++++++|+++|++ ||.|.+|.|+.++ ++.++|||||+|.+.++|.+|++.+ +.. ++|+.|.|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            34589999999999999999999999 9999999999998 8999999999999999999999987 567 999999999


Q ss_pred             eccCCCCC
Q psy15852        259 KATPKPEP  266 (661)
Q Consensus       259 ~a~~k~~~  266 (661)
                      ++.++...
T Consensus        86 ~a~~~~~~   93 (104)
T 2dhg_A           86 VAIPKASR   93 (104)
T ss_dssp             BCCCCCSC
T ss_pred             EccCCCcC
Confidence            99876644

>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=99.57  E-value=2.5e-15  Score=128.71  Aligned_cols=80  Identities=9%  Similarity=0.180  Sum_probs=73.3

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      ..++|||+|||+++++++|+++|++||.+ .|.|++++ +++++|||||+|.+.++|++||+.++..|+|+.|.|.++.+
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~~~   91 (102)
T 1wez_A           14 TGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNST   91 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECCC
Confidence            45799999999999999999999999955 99999998 79999999999999999999997667899999999999886


Q ss_pred             CC
Q psy15852        263 KP  264 (661)
Q Consensus       263 k~  264 (661)
                      ..
T Consensus        92 ~~   93 (102)
T 1wez_A           92 AG   93 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

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

Probab=99.57  E-value=6e-15  Score=126.72  Aligned_cols=82  Identities=21%  Similarity=0.368  Sum_probs=76.4

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||+.+++++|+++|++||.|..|.|+.+  ++.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2d9p_A           14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ   91 (103)
T ss_dssp             SCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEec
Confidence            4589999999999999999999999999999999987  6899999999999999999999975 788999999999999


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++..+
T Consensus        92 ~~~~~   96 (103)
T 2d9p_A           92 RKEER   96 (103)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87654

>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=99.57  E-value=6.5e-15  Score=126.96  Aligned_cols=84  Identities=21%  Similarity=0.311  Sum_probs=76.8

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC---eEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND---KEVDV  257 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g---~~i~V  257 (661)
                      +..++|||+|||..+++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|.+|++.+ +..+.|   +.|.|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            346899999999999999999999999999999999987 6999999999999999999999976 677787   99999


Q ss_pred             EeccCCCCC
Q psy15852        258 KKATPKPEP  266 (661)
Q Consensus       258 ~~a~~k~~~  266 (661)
                      .++.++..+
T Consensus        92 ~~a~~~~~~  100 (105)
T 2dnh_A           92 KFADTDKES  100 (105)
T ss_dssp             EESCSSCCC
T ss_pred             EECccCccc
Confidence            999987754

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

Probab=99.57  E-value=6.9e-15  Score=128.62  Aligned_cols=85  Identities=18%  Similarity=0.279  Sum_probs=78.3

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeE--------EEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNII--------ETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND  252 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~--------~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g  252 (661)
                      ...++|||+|||.++++++|+++|++||.|.        .|.|+.++.+++++|||||+|.+.++|.+|++.+ +..|.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   92 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCC
Confidence            3458999999999999999999999999999        6999999889999999999999999999999975 789999


Q ss_pred             eEEEEEeccCCCCC
Q psy15852        253 KEVDVKKATPKPEP  266 (661)
Q Consensus       253 ~~i~V~~a~~k~~~  266 (661)
                      +.|.|.++.++...
T Consensus        93 ~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           93 SKLKVSLARKKPPM  106 (113)
T ss_dssp             EECEEECSSCCCCS
T ss_pred             CEEEEEECCCCCCC
Confidence            99999999887643

>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=99.57  E-value=1.7e-15  Score=122.04  Aligned_cols=75  Identities=37%  Similarity=0.758  Sum_probs=72.0

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      +|||+|||+++++++|+++|++||+|.+|.+++++.++.++|||||+|.+.++|.+|++.+++.+.|+.|.|++|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999998889999999999875

>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=99.57  E-value=3.1e-15  Score=129.64  Aligned_cols=84  Identities=20%  Similarity=0.404  Sum_probs=78.2

Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                      .+..++|||+|||..+++++|+++|++||.|..|.+++++.++.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            445689999999999999999999999999999999999889999999999999999999999865 7899999999999


Q ss_pred             ccCCC
Q psy15852        260 ATPKP  264 (661)
Q Consensus       260 a~~k~  264 (661)
                      +.++.
T Consensus       103 a~~k~  107 (108)
T 2jrs_A          103 VTERT  107 (108)
T ss_dssp             SCSSC
T ss_pred             cccCC
Confidence            98764

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

Probab=99.57  E-value=5.5e-15  Score=126.70  Aligned_cols=61  Identities=20%  Similarity=0.296  Sum_probs=58.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      .++|||+|||+++|+++|+++|++||.|.+|+|++|+. |+++|||||+|.+.++|.+|++.
T Consensus        11 ~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~   71 (103)
T 1s79_A           11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVET   71 (103)
T ss_dssp             GGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHc
Confidence            57899999999999999999999999999999999988 99999999999999999999994

>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=99.57  E-value=5.6e-15  Score=127.59  Aligned_cols=84  Identities=21%  Similarity=0.419  Sum_probs=77.1

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCcc---CCeEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKI---NDKEVDV  257 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~---~g~~i~V  257 (661)
                      ...++|||+|||..+++++|+++|++||.|.+|.|+.++.+++++|||||+|.+.++|.+|++.+ +..+   .|+.|.|
T Consensus        11 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v   90 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQV   90 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEE
Confidence            34589999999999999999999999999999999999999999999999999999999999976 5566   8899999


Q ss_pred             EeccCCCC
Q psy15852        258 KKATPKPE  265 (661)
Q Consensus       258 ~~a~~k~~  265 (661)
                      .++.++..
T Consensus        91 ~~a~~~~~   98 (106)
T 2dgp_A           91 KPADSESR   98 (106)
T ss_dssp             EECCCCSC
T ss_pred             EECCcccc
Confidence            99988654

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

Probab=99.56  E-value=5.8e-15  Score=124.74  Aligned_cols=80  Identities=18%  Similarity=0.379  Sum_probs=75.3

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||+.+++++|+++|++||.|..|.+++++.++.++|||||+|.+.++|.+|++.+ +..++|++|.|.++.
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   93 (95)
T 2cqc_A           14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPS   93 (95)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecC
Confidence            3578999999999999999999999999999999999999999999999999999999999975 689999999999987


Q ss_pred             C
Q psy15852        262 P  262 (661)
Q Consensus       262 ~  262 (661)
                      +
T Consensus        94 ~   94 (95)
T 2cqc_A           94 S   94 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.56  E-value=6.2e-15  Score=122.33  Aligned_cols=81  Identities=21%  Similarity=0.348  Sum_probs=71.7

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..+.|+.|.|.
T Consensus         6 ~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l~v~   81 (87)
T 3bs9_A            6 HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA----IQQMGGQWLGGRQIRTN   81 (87)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHH----HHHcCCCEECCeEEEEE
Confidence            34455555555999999999999999999999999988999999999999999999999    88899999999999999


Q ss_pred             hhhcc
Q psy15852        179 KAKAK  183 (661)
Q Consensus       179 ~~~~~  183 (661)
                      ++.++
T Consensus        82 ~a~~k   86 (87)
T 3bs9_A           82 WATRK   86 (87)
T ss_dssp             EEC--
T ss_pred             ecCCC
Confidence            88764

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

Probab=99.56  E-value=3.9e-15  Score=123.05  Aligned_cols=66  Identities=17%  Similarity=0.244  Sum_probs=62.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      ..++|||+|||+++++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|.+|++.+|.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   69 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA   69 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcC
Confidence            468999999999999999999999999999999999999999999999999999999999997553

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

Probab=99.56  E-value=5.2e-15  Score=127.83  Aligned_cols=81  Identities=19%  Similarity=0.348  Sum_probs=76.6

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      .++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++.+
T Consensus        23 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~  102 (106)
T 1p27_B           23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV  102 (106)
T ss_dssp             BEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecC
Confidence            478999999999999999999999999999999999999999999999999999999999975 7899999999999987


Q ss_pred             CC
Q psy15852        263 KP  264 (661)
Q Consensus       263 k~  264 (661)
                      +.
T Consensus       103 ~~  104 (106)
T 1p27_B          103 RG  104 (106)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>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=99.56  E-value=8.6e-15  Score=125.74  Aligned_cols=66  Identities=29%  Similarity=0.438  Sum_probs=62.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      ..++|||+|||+++++++|+++|++||.|.+|+|++++.||+++|||||+|.+.++|.+|+++.|.
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~   79 (103)
T 2cqg_A           14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHM   79 (103)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEE
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHcCCe
Confidence            467899999999999999999999999999999999999999999999999999999999997543

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

Probab=99.56  E-value=5.9e-15  Score=128.12  Aligned_cols=67  Identities=30%  Similarity=0.464  Sum_probs=61.7

Q ss_pred             cCCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        591 EAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       591 ~~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      ...++|||+|||+++|+++|+++|++||.|.+|+|++++.||+++|||||+|.+.++|.+|++.+++
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~   89 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRH   89 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCC
Confidence            4568999999999999999999999999999999999999999999999999999999999998653

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=5.7e-15  Score=125.83  Aligned_cols=80  Identities=16%  Similarity=0.192  Sum_probs=72.0

Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC---CCccCCeEEEE
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP---KQKINDKEVDV  257 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~---~~~~~g~~i~V  257 (661)
                      .+..++|||+|||+++++++|+++|++||.|.+|.|+++      +|||||+|.+.++|.+|++.+   +..+.|++|.|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345689999999999999999999999999999999864      799999999999999999964   36899999999


Q ss_pred             EeccCCCCC
Q psy15852        258 KKATPKPEP  266 (661)
Q Consensus       258 ~~a~~k~~~  266 (661)
                      .++.++...
T Consensus        87 ~~A~~~~~~   95 (105)
T 1sjq_A           87 QFSNHKELK   95 (105)
T ss_dssp             CCCSSSSCC
T ss_pred             EEcCCCCCC
Confidence            999887654

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

Probab=99.56  E-value=8.3e-15  Score=124.84  Aligned_cols=67  Identities=18%  Similarity=0.127  Sum_probs=63.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCee-EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIE-NVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~-~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ..++|||+|||+++++++|+++|++||.|. +|+|++|+.||+++|||||+|.+.++|++|++.++..
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   75 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGK   75 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTS
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCC
Confidence            468999999999999999999999999999 9999999999999999999999999999999987653

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

Probab=99.56  E-value=3.3e-15  Score=120.90  Aligned_cols=63  Identities=32%  Similarity=0.503  Sum_probs=61.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        594 NKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       594 ~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      ++|||+|||+++++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|.+|++.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~   63 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR   63 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC
Confidence            479999999999999999999999999999999999999999999999999999999999877

>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=99.56  E-value=8e-15  Score=121.93  Aligned_cols=82  Identities=21%  Similarity=0.428  Sum_probs=75.4

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCC-cCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQ-RKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~-~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +.++|||+|||.++++++|+++|++||.|.+|.++.+..++. ++|||||+|.+.++|.+|++.+ +..++|+.|.|.++
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            457899999999999999999999999999999999887665 8999999999999999999975 78999999999999


Q ss_pred             cCCC
Q psy15852        261 TPKP  264 (661)
Q Consensus       261 ~~k~  264 (661)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.55  E-value=1.3e-14  Score=124.78  Aligned_cols=83  Identities=20%  Similarity=0.348  Sum_probs=76.1

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEE-EEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIE-TEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~-v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+++++++|+++|++||.|.. |.|+.+ .+++++|||||+|.+.++|++||+.++..++|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEEC
Confidence            34589999999999999999999999999997 888888 6799999999999999999999999788999999999998


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .++..
T Consensus        92 ~~~~~   96 (104)
T 1wg5_A           92 SRAEV   96 (104)
T ss_dssp             CTTTS
T ss_pred             CHHHH
Confidence            87553

>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=99.55  E-value=1e-14  Score=126.91  Aligned_cols=83  Identities=17%  Similarity=0.342  Sum_probs=77.4

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|++.+ +..++|+.|.|.++.
T Consensus        25 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  104 (110)
T 1oo0_B           25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF  104 (110)
T ss_dssp             TBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcc
Confidence            3478999999999999999999999999999999999989999999999999999999999975 789999999999998


Q ss_pred             CCCC
Q psy15852        262 PKPE  265 (661)
Q Consensus       262 ~k~~  265 (661)
                      ++..
T Consensus       105 ~~~~  108 (110)
T 1oo0_B          105 VKGP  108 (110)
T ss_dssp             ESSC
T ss_pred             cCCC
Confidence            7653

>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=99.55  E-value=1.1e-14  Score=119.60  Aligned_cols=80  Identities=19%  Similarity=0.263  Sum_probs=72.8

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      ++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..+.|++|.|.++
T Consensus         3 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a----~~~l~g~~~~g~~l~v~~a   78 (83)
T 3md1_A            3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA----MDSMQGQDLNGRPLRINWA   78 (83)
T ss_dssp             EEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHH----HHHHTTCEETTEECEEEEC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHH----HHHhcCCeeCCcEEEEEec
Confidence            455555556999999999999999999999999989999999999999999999999    8889999999999999998


Q ss_pred             hccC
Q psy15852        181 KAKS  184 (661)
Q Consensus       181 ~~~~  184 (661)
                      .++.
T Consensus        79 ~~~~   82 (83)
T 3md1_A           79 AKLE   82 (83)
T ss_dssp             CCCC
T ss_pred             CcCC
Confidence            7653

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

Probab=99.55  E-value=6.9e-15  Score=125.31  Aligned_cols=83  Identities=17%  Similarity=0.351  Sum_probs=76.9

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeE-EEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeE----E
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNII-ETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKE----V  255 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~-~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~----i  255 (661)
                      ...++|||+|||+++++++|+++|++||.|. +|.+++++.++.++|||||+|.+.++|++|++.+ +..+.|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            3468999999999999999999999999999 9999999989999999999999999999999976 68899999    9


Q ss_pred             EEEeccCCC
Q psy15852        256 DVKKATPKP  264 (661)
Q Consensus       256 ~V~~a~~k~  264 (661)
                      +|.++.+..
T Consensus        87 ~v~~a~~~~   95 (99)
T 2div_A           87 KLNYATYSG   95 (99)
T ss_dssp             CEEETTCCS
T ss_pred             EEeecCCCC
Confidence            999998653

>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=99.55  E-value=2e-14  Score=124.78  Aligned_cols=81  Identities=19%  Similarity=0.379  Sum_probs=73.0

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.+   +.++|||||+|.+.++|++|++.+ +..++|+.|.|.++
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            34589999999999999999999999999999999764   557999999999999999999775 68999999999999


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .++..
T Consensus        97 ~~~~~  101 (109)
T 1x4a_A           97 RSGRG  101 (109)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            87653

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

Probab=99.55  E-value=5.9e-15  Score=118.80  Aligned_cols=59  Identities=29%  Similarity=0.545  Sum_probs=57.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHH
Q psy15852        595 KMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASV  653 (661)
Q Consensus       595 ~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~  653 (661)
                      +|||+|||+++++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|++|++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~   59 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE   59 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999999998

>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=99.55  E-value=2.2e-14  Score=123.13  Aligned_cols=83  Identities=25%  Similarity=0.384  Sum_probs=74.8

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+.+++++|+++|++||.|..|.|++++.+  ++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            34589999999999999999999999999999999998643  6899999999999999999965 67899999999999


Q ss_pred             cCCCCC
Q psy15852        261 TPKPEP  266 (661)
Q Consensus       261 ~~k~~~  266 (661)
                      .++...
T Consensus        91 ~~~~~~   96 (103)
T 2cqi_A           91 TTPSSQ   96 (103)
T ss_dssp             CCTTCC
T ss_pred             CCCccc
Confidence            886543

>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=99.55  E-value=2.8e-14  Score=122.46  Aligned_cols=83  Identities=20%  Similarity=0.458  Sum_probs=75.4

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.+..  .++|||||+|.+.++|.+|++.+ +..|+|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3458999999999999999999999999999999998864  38999999999999999999975 78999999999999


Q ss_pred             cCCCCC
Q psy15852        261 TPKPEP  266 (661)
Q Consensus       261 ~~k~~~  266 (661)
                      .++...
T Consensus        91 ~~~~~~   96 (103)
T 2cq3_A           91 TARVMT   96 (103)
T ss_dssp             CSSCCC
T ss_pred             ccCCCC
Confidence            987654

>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=99.55  E-value=6.1e-15  Score=126.30  Aligned_cols=60  Identities=18%  Similarity=0.163  Sum_probs=56.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      ..+|||+|||+++||+||+++|++|| |++|+|++|+ +|+++|||||+|.+.++|++||+.
T Consensus        15 ~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~   74 (102)
T 1wez_A           15 GHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAK   74 (102)
T ss_dssp             SCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh
Confidence            57999999999999999999999999 4599999998 799999999999999999999964

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

Probab=99.54  E-value=1.6e-14  Score=126.91  Aligned_cols=67  Identities=24%  Similarity=0.417  Sum_probs=63.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|++++.|++++|||||+|.+.++|.+|++.+++.
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~   82 (116)
T 2cqd_A           16 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPI   82 (116)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCc
Confidence            4689999999999999999999999999999999999999999999999999999999999987763

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

Probab=99.54  E-value=1.7e-14  Score=128.44  Aligned_cols=81  Identities=17%  Similarity=0.335  Sum_probs=75.4

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK  263 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k  263 (661)
                      .++|||+|||.++++++|+++|++||.|.+|.+++++.++.++|||||+|.+.++|.+|++.++..|+|+.|.|.++.+.
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~  115 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRTN  115 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCCC
Confidence            47999999999999999999999999999999999988899999999999999999999944478999999999999865


Q ss_pred             C
Q psy15852        264 P  264 (661)
Q Consensus       264 ~  264 (661)
                      .
T Consensus       116 ~  116 (124)
T 2jwn_A          116 M  116 (124)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.54  E-value=1.5e-14  Score=124.43  Aligned_cols=62  Identities=31%  Similarity=0.285  Sum_probs=59.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeE-EEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIEN-VTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~-v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      ...+|||+|||+++|++||+++|++||.|.+ |+|+.+ .||+++|||||+|.+.++|.+||..
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~   76 (104)
T 1wg5_A           14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK   76 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh
Confidence            4679999999999999999999999999987 999998 6899999999999999999999998

>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=99.54  E-value=8e-15  Score=128.43  Aligned_cols=81  Identities=11%  Similarity=0.087  Sum_probs=76.2

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCe-EEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNI-IETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i-~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||+++++++|+++|++||.| ..|.|++++ +++++|||||+|.+.++|.+||+.++..|.|+.|.|.++.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~a~   92 (114)
T 2cpy_A           14 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVT   92 (114)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEEC
T ss_pred             CccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEECC
Confidence            45799999999999999999999999999 899999998 8999999999999999999999997789999999999998


Q ss_pred             CCC
Q psy15852        262 PKP  264 (661)
Q Consensus       262 ~k~  264 (661)
                      ++.
T Consensus        93 ~~~   95 (114)
T 2cpy_A           93 LED   95 (114)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            765

>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=99.54  E-value=3.1e-15  Score=134.70  Aligned_cols=82  Identities=13%  Similarity=0.202  Sum_probs=75.1

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCC---eEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGN---IIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~---i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~  258 (661)
                      ...++|||+|||+++|+++|+++|++||.   |.+|.|++++. |+++|||||+|.+.++|++||+.++..|+|+.|.|.
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVF  120 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEEE
Confidence            44589999999999999999999999999   89999999987 999999999999999999999955689999999999


Q ss_pred             eccCCC
Q psy15852        259 KATPKP  264 (661)
Q Consensus       259 ~a~~k~  264 (661)
                      ++.++.
T Consensus       121 ~a~~~e  126 (136)
T 2hgl_A          121 KSHRTE  126 (136)
T ss_dssp             ECCHHH
T ss_pred             ECChHH
Confidence            987643

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

Probab=99.54  E-value=4.9e-14  Score=123.37  Aligned_cols=82  Identities=18%  Similarity=0.272  Sum_probs=75.3

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||.++++++|+++|++||.|.+|.|+.++ +++++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            345899999999999999999999999999999999987 4899999999999999999999975 78999999999998


Q ss_pred             cCCC
Q psy15852        261 TPKP  264 (661)
Q Consensus       261 ~~k~  264 (661)
                      ....
T Consensus        92 ~~~~   95 (114)
T 2do0_A           92 ERAL   95 (114)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            7644

>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=99.54  E-value=3e-14  Score=123.69  Aligned_cols=84  Identities=18%  Similarity=0.354  Sum_probs=77.5

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCC-eEEEEec-cCCCCCCcCcEEEEEeCCHHHHHHHHHhC---CCccCCeEEEE
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGN-IIETEMP-YDKSKSQRKNFCFITFEHESVVIDLLKNP---KQKINDKEVDV  257 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~-i~~v~i~-~~~~~g~~~g~afV~f~~~~~A~~Al~~~---~~~~~g~~i~V  257 (661)
                      ..++|||+|||+++++++|+++|++||. |.+|.++ .+..++.++|||||+|.+.++|.+|++.+   +..++|+.|.|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V   86 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   86 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEE
Confidence            4579999999999999999999999998 9999998 88888999999999999999999999986   37899999999


Q ss_pred             EeccCCCCC
Q psy15852        258 KKATPKPEP  266 (661)
Q Consensus       258 ~~a~~k~~~  266 (661)
                      .++.++...
T Consensus        87 ~~a~~~~~~   95 (109)
T 2dis_A           87 DWAEPEIDV   95 (109)
T ss_dssp             EESCSSCST
T ss_pred             EEcCCCCCc
Confidence            999987654

>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=99.54  E-value=9.2e-15  Score=130.87  Aligned_cols=83  Identities=18%  Similarity=0.360  Sum_probs=77.7

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +..++|||+|||+++++++|+++|++||+|..|.+++++.+++++|||||+|.+.++|++|++.+ +..|+|++|.|.++
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a  123 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS  123 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            44589999999999999999999999999999999999999999999999999999999999975 68999999999999


Q ss_pred             cCCC
Q psy15852        261 TPKP  264 (661)
Q Consensus       261 ~~k~  264 (661)
                      .++.
T Consensus       124 ~~~~  127 (129)
T 2kxn_B          124 ITKR  127 (129)
T ss_dssp             SSSS
T ss_pred             cCCC
Confidence            8764

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

Probab=99.54  E-value=1.2e-14  Score=123.89  Aligned_cols=80  Identities=20%  Similarity=0.284  Sum_probs=74.8

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEE--------EEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIE--------TEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND  252 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~--------v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g  252 (661)
                      +..++|||+|||.++++++|+++|++||.|..        |.++.++.+++++|||||+|.+.++|.+|++.+ +..+.|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            44589999999999999999999999999999        999999999999999999999999999999875 789999


Q ss_pred             eEEEEEecc
Q psy15852        253 KEVDVKKAT  261 (661)
Q Consensus       253 ~~i~V~~a~  261 (661)
                      +.|.|.+|+
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999874

>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=99.53  E-value=4.9e-15  Score=119.25  Aligned_cols=63  Identities=32%  Similarity=0.524  Sum_probs=60.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        595 KMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       595 ~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      +|||+|||+++|+++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|.+|++...+
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~   63 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYH   63 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCC
Confidence            589999999999999999999999999999999999999999999999999999999997443

>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=99.53  E-value=3.8e-15  Score=124.58  Aligned_cols=79  Identities=15%  Similarity=0.183  Sum_probs=69.0

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCC--CeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYG--EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G--~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ++++.++++++++++|+++|++||  .|.+|+|++++.+|+++|||||+|.+.++|++|    +..+|+..+.|+.|.|.
T Consensus         3 ~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~A----i~~l~g~~~~gr~i~V~   78 (90)
T 3p5t_L            3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL----MDLLPKRELHGQNPVVT   78 (90)
T ss_dssp             -CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHH----HHHGGGSCSSSCCCEEC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHH----HHHcCCCeeCCEEEEEE
Confidence            455555556999999999999999  999999999999999999999999999999999    88999999999999999


Q ss_pred             hhhcc
Q psy15852        179 KAKAK  183 (661)
Q Consensus       179 ~~~~~  183 (661)
                      ++.+.
T Consensus        79 ~~~~~   83 (90)
T 3p5t_L           79 PSNKL   83 (90)
T ss_dssp             CC---
T ss_pred             ECCCC
Confidence            88764

>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=99.53  E-value=8.3e-15  Score=125.10  Aligned_cols=82  Identities=20%  Similarity=0.387  Sum_probs=73.9

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCC-CCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDK-SKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||.++++++|+++|++|| |.+|.|++++ .+++++|||||+|.+.++|.+|+...+..++|+.|.|.++
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~~a   95 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVA   95 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEEec
Confidence            3458999999999999999999999999 9999999998 6899999999999999999999944478999999999999


Q ss_pred             cCCC
Q psy15852        261 TPKP  264 (661)
Q Consensus       261 ~~k~  264 (661)
                      .++.
T Consensus        96 ~~~~   99 (100)
T 2j76_E           96 DQAQ   99 (100)
T ss_dssp             CCSC
T ss_pred             cCCC
Confidence            8764

>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=99.53  E-value=1.6e-14  Score=122.27  Aligned_cols=81  Identities=25%  Similarity=0.344  Sum_probs=73.5

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +++++.++++++++++|+++|++||+|.+|+|+.++.+|+++|||||+|.+.++|++|    +..+++..+.|+.|.|.+
T Consensus         3 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A----i~~l~g~~~~g~~l~V~~   78 (96)
T 2x1f_A            3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA----VRNLNGYQLGSRFLKCGY   78 (96)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHH----HHHHTTCEETTEECEEEE
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHH----HHHhCCCeECCeEEEEEE
Confidence            4555555556999999999999999999999999998999999999999999999999    889999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        79 a~~~~   83 (96)
T 2x1f_A           79 SSNSD   83 (96)
T ss_dssp             CSCSS
T ss_pred             cCCCC
Confidence            87654

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

Probab=99.53  E-value=1.2e-14  Score=134.46  Aligned_cols=82  Identities=22%  Similarity=0.386  Sum_probs=76.2

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCC--CeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFG--NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G--~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                      ..++|||+|||+++++++|+++|++||  .|.+|.|+.|+.+|+++|||||+|.+.++|.+||+.+ +..|+|+.|.|.+
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  9999999999999999999999999999999999996 6899999999999


Q ss_pred             ccCCC
Q psy15852        260 ATPKP  264 (661)
Q Consensus       260 a~~k~  264 (661)
                      +.++.
T Consensus       134 a~~~~  138 (156)
T 3n9u_C          134 ATRQN  138 (156)
T ss_dssp             CCHHH
T ss_pred             cCCCc
Confidence            97643

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

Probab=99.53  E-value=4.1e-15  Score=127.01  Aligned_cols=81  Identities=20%  Similarity=0.299  Sum_probs=73.7

Q ss_pred             CCcEEEEcCCC------cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecc
Q psy15852         99 KNKMVSHPGIV------HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN  172 (661)
Q Consensus        99 ~~~~~~~~~~~------~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g  172 (661)
                      .+++||.++++      ++++++|+++|++||+|.+|+|++++.||++||||||+|.+.++|++|    +..+|+..+.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~A----i~~lng~~~~g   81 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKI----IKSFHGKRLDL   81 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHH----HHHHTTCBSSS
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHH----HHHhCCcccCC
Confidence            34566666777      899999999999999999999999999999999999999999999999    88999999999


Q ss_pred             -eeehhhhhhcc
Q psy15852        173 -KKIEAKKAKAK  183 (661)
Q Consensus       173 -~~i~v~~~~~~  183 (661)
                       +.|.|.++.+.
T Consensus        82 ~r~l~V~~a~~~   93 (100)
T 3ns6_A           82 KHRLFLYTMKDV   93 (100)
T ss_dssp             SCBCEEEESHHH
T ss_pred             CeEEEEEECchh
Confidence             99999988754

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

Probab=99.53  E-value=1.7e-14  Score=121.83  Aligned_cols=82  Identities=22%  Similarity=0.430  Sum_probs=73.7

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..+.|++|.|.
T Consensus         5 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~V~   80 (95)
T 2dnz_A            5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA----LEQLNGFELAGRPMRVG   80 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHH----HHHHTTCCSSSSCCEEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHH----HHHhCCCeeCCcEEEEE
Confidence            34555555555999999999999999999999999999999999999999999999999    88899999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        81 ~a~~~~   86 (95)
T 2dnz_A           81 HVTERL   86 (95)
T ss_dssp             ESSCCC
T ss_pred             Eccccc
Confidence            987654

>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=99.53  E-value=1.3e-14  Score=119.74  Aligned_cols=79  Identities=23%  Similarity=0.305  Sum_probs=70.5

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..+.|++|.|.
T Consensus         7 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A            7 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA----IDNMNESELFGRTIRVN   82 (85)
T ss_dssp             SSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHH----HHHhCCCEECCcEEEEE
Confidence            34455555555999999999999999999999999988999999999999999999999    88999999999999998


Q ss_pred             hhh
Q psy15852        179 KAK  181 (661)
Q Consensus       179 ~~~  181 (661)
                      +++
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            763

>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=4.5e-14  Score=121.21  Aligned_cols=77  Identities=19%  Similarity=0.430  Sum_probs=70.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||+++++++|+++|++||.|..|.++        ++||||+|.+.++|.+|++.+ +..+.|+.|.|.++.
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   81 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAK   81 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcC
Confidence            45799999999999999999999999999999986        569999999999999999975 688999999999998


Q ss_pred             CCCCCC
Q psy15852        262 PKPEPF  267 (661)
Q Consensus       262 ~k~~~~  267 (661)
                      ++....
T Consensus        82 ~~~~~~   87 (103)
T 2dgu_A           82 PPDQKR   87 (103)
T ss_dssp             CCCCCC
T ss_pred             CCcccc
Confidence            876543

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

Probab=99.53  E-value=2e-14  Score=121.16  Aligned_cols=77  Identities=16%  Similarity=0.200  Sum_probs=69.3

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCC-C--ccCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPK-Q--KINDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~-~--~~~g~~i~V~  258 (661)
                      +++++|||+|||+++++++|+++|++||.|.+|.+++      .||||||+|.+.++|.+|++.++ .  .+.|++|.|.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            4568999999999999999999999999999999975      37999999999999999999863 3  5899999999


Q ss_pred             eccCCC
Q psy15852        259 KATPKP  264 (661)
Q Consensus       259 ~a~~k~  264 (661)
                      +++++.
T Consensus        93 ~S~~k~   98 (100)
T 3r27_A           93 YSTSQK   98 (100)
T ss_dssp             ECSCSC
T ss_pred             eccccc
Confidence            998764

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

Probab=99.53  E-value=1.4e-14  Score=127.68  Aligned_cols=79  Identities=24%  Similarity=0.426  Sum_probs=74.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||+++++++|+++|++||.|.+|.+++++.+++++|||||+|.+.++|.+|++.+ +..++|+.|+|.+++
T Consensus        39 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~ak  118 (118)
T 2khc_A           39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK  118 (118)
T ss_dssp             CSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC-
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            3479999999999999999999999999999999999989999999999999999999999986 689999999999874

>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=99.53  E-value=2.2e-14  Score=121.42  Aligned_cols=80  Identities=18%  Similarity=0.255  Sum_probs=73.3

Q ss_pred             cCCeeEecCCCccCCHHHHH----HHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEE
Q psy15852        183 KSGKIFVGGLSPEMKDEEIK----AHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDV  257 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~----~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V  257 (661)
                      ..++|||+|||+++++++|+    ++|++||+|.+|.|+.++.+   +|||||+|.+.++|++|++.+ +..++|+.|.|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            45789999999999999999    99999999999999998765   899999999999999999976 67899999999


Q ss_pred             EeccCCCC
Q psy15852        258 KKATPKPE  265 (661)
Q Consensus       258 ~~a~~k~~  265 (661)
                      .++.++..
T Consensus        85 ~~a~~~~~   92 (96)
T 2dgx_A           85 SLATGASG   92 (96)
T ss_dssp             EECCCSSC
T ss_pred             EEcCCCCC
Confidence            99987654

>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=99.53  E-value=1e-14  Score=125.45  Aligned_cols=82  Identities=18%  Similarity=0.481  Sum_probs=77.0

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      .++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++.+
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   87 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCC
Confidence            478999999999999999999999999999999999888999999999999999999999876 6889999999999988


Q ss_pred             CCC
Q psy15852        263 KPE  265 (661)
Q Consensus       263 k~~  265 (661)
                      +..
T Consensus        88 ~~~   90 (104)
T 1p1t_A           88 EKN   90 (104)
T ss_dssp             TTH
T ss_pred             ccc
Confidence            654

>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=99.53  E-value=1.1e-14  Score=127.49  Aligned_cols=81  Identities=12%  Similarity=0.272  Sum_probs=75.9

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK  263 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k  263 (661)
                      .++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||..++..|+|+.|.|.++.++
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~~~  104 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAE  104 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecCCC
Confidence            37999999999999999999999999999999999999999999999999999999999944578999999999999876


Q ss_pred             C
Q psy15852        264 P  264 (661)
Q Consensus       264 ~  264 (661)
                      .
T Consensus       105 ~  105 (114)
T 2cq4_A          105 K  105 (114)
T ss_dssp             H
T ss_pred             c
Confidence            5

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.53  E-value=1.2e-14  Score=118.85  Aligned_cols=63  Identities=17%  Similarity=0.306  Sum_probs=58.3

Q ss_pred             CeEEEcCCCCCC------CHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        594 NKMVSHPGIVDK------ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       594 ~~l~v~nlp~~~------te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ++|||+|||+++      |+++|+++|++||.|.+|+|+  +.||+++|||||+|.+.++|.+|++.++..
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~   70 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGY   70 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCc
Confidence            689999999999      789999999999999999988  367999999999999999999999987654

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

Probab=99.53  E-value=2.4e-14  Score=120.90  Aligned_cols=81  Identities=25%  Similarity=0.421  Sum_probs=73.4

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      +..++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..+.|++|.|
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA----KERANGMELDGRRIRV   89 (95)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHH----HHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHH----HHHhCCCEECCEEEEE
Confidence            345566666666999999999999999999999999999999999999999999999999    8889999999999999


Q ss_pred             hhhhc
Q psy15852        178 KKAKA  182 (661)
Q Consensus       178 ~~~~~  182 (661)
                      .++++
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            88764

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

Probab=99.53  E-value=1.9e-14  Score=120.81  Aligned_cols=82  Identities=18%  Similarity=0.324  Sum_probs=75.2

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +..++|||+|||.++++++|+++|++||.|..|.++++  ++.++|||||+|.+.++|.+|++.+ +..++|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45689999999999999999999999999999999874  6889999999999999999999975 68899999999999


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .+...
T Consensus        84 ~~~~~   88 (92)
T 2dgv_A           84 RNASG   88 (92)
T ss_dssp             SCCSS
T ss_pred             CCCCC
Confidence            87654

>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=99.53  E-value=1.5e-14  Score=122.11  Aligned_cols=80  Identities=20%  Similarity=0.385  Sum_probs=74.0

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+.+++++|+++|++||+|.+|.++.++. ++++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            3457999999999999999999999999999999999886 899999999999999999999965 78999999999998


Q ss_pred             cC
Q psy15852        261 TP  262 (661)
Q Consensus       261 ~~  262 (661)
                      ..
T Consensus        93 ~~   94 (95)
T 2ywk_A           93 SS   94 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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=99.52  E-value=1.3e-14  Score=125.07  Aligned_cols=87  Identities=21%  Similarity=0.216  Sum_probs=76.7

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ...++++.++++++++++|+++|++||+|.+|+|+.++.+++++|||||+|.+.++|++|    +..+++..|.|+.|.|
T Consensus        14 ~~~~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           14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA----IKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHH----HHHSSSCBCSSCBCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHH----HHHhCCCeECCeEEEE
Confidence            334555555555999999999999999999999999998999999999999999999999    8889999999999999


Q ss_pred             hhhhccCCeeE
Q psy15852        178 KKAKAKSGKIF  188 (661)
Q Consensus       178 ~~~~~~~~~lf  188 (661)
                      .++.++..+..
T Consensus        90 ~~a~~~~~~~~  100 (105)
T 1x5u_A           90 NKASAHNKNLS  100 (105)
T ss_dssp             EETTTTSCCCC
T ss_pred             EECCCCCcCCC
Confidence            99988765543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=2.9e-14  Score=119.43  Aligned_cols=81  Identities=12%  Similarity=0.314  Sum_probs=74.8

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      ..++|||+|||+++++++|+++|++| .|..|.|+++ .+++++|||||+|.+.++|.+|++.++..++|+.|.|.++.+
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a~~   86 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREKS   86 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEESS
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEECCc
Confidence            45799999999999999999999999 9999999998 679999999999999999999999446899999999999988


Q ss_pred             CCC
Q psy15852        263 KPE  265 (661)
Q Consensus       263 k~~  265 (661)
                      ++.
T Consensus        87 ~~~   89 (91)
T 2dgw_A           87 GPS   89 (91)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

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

Probab=99.52  E-value=2.4e-14  Score=120.62  Aligned_cols=80  Identities=30%  Similarity=0.405  Sum_probs=72.4

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ...++++.++++++++++|+++|++||+|.+|+|+.++.+++++|||||+|.+.++|++|    +..+++..+.|++|.|
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l~v   90 (94)
T 2e5h_A           15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC----TRAINNKQLFGRVIKA   90 (94)
T ss_dssp             CTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHH----HHHTTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHH----HHHcCCCeeCCcEEEE
Confidence            345666666666999999999999999999999999999999999999999999999999    8899999999999999


Q ss_pred             hhhh
Q psy15852        178 KKAK  181 (661)
Q Consensus       178 ~~~~  181 (661)
                      .+++
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            8763

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

Probab=99.52  E-value=2.4e-14  Score=116.32  Aligned_cols=70  Identities=19%  Similarity=0.162  Sum_probs=63.0

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      -+++.++.+.+||++|+++|.+||+|.++++..      +||||||+|.++++|++|    +..+|+..+.|++|.|..+
T Consensus         9 wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~A----i~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            9 WLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKA----QMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             EEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHH----HHHHTTEEETTEEEEEECC
T ss_pred             eEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHH----HHHhcCCEECCcEEEEEEC
Confidence            355555556999999999999999999999975      689999999999999999    9999999999999998766

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

Probab=99.52  E-value=2.1e-14  Score=122.29  Aligned_cols=81  Identities=35%  Similarity=0.490  Sum_probs=72.4

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +. +++..+.|+.|.|.
T Consensus        10 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A----~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A           10 SNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA----VN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHH----HH-HCCCBSSSCBCEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHH----HH-hCCCEECCeEEEEE
Confidence            34555555556999999999999999999999999999999999999999999999998    66 89999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        85 ~a~~~~   90 (99)
T 2dgs_A           85 RAEPRD   90 (99)
T ss_dssp             ECCCCC
T ss_pred             ECCCCc
Confidence            987654

>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=99.52  E-value=1.8e-14  Score=122.71  Aligned_cols=81  Identities=22%  Similarity=0.344  Sum_probs=72.9

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..+.|++|.|.+
T Consensus         9 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA----YAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHH----HHHTTTEESSSCEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHH----HHHhCCCEECCcEEEEEE
Confidence            4455555555999999999999999999999999998899999999999999999999    889999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        85 a~~~~   89 (99)
T 1whw_A           85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            87654

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

Probab=99.52  E-value=1.8e-14  Score=123.78  Aligned_cols=82  Identities=24%  Similarity=0.380  Sum_probs=73.3

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..|.|+.|.|.
T Consensus        15 ~~~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           15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA----IAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             SEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHH----HHHTTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHH----HHHcCCCeeCCcEEEEE
Confidence            34455555555999999999999999999999999998999999999999999999999    88899999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        91 ~a~~~~   96 (103)
T 2cq0_A           91 WAKPST   96 (103)
T ss_dssp             ESSCCC
T ss_pred             ECCCCC
Confidence            987654

>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=99.52  E-value=8.4e-15  Score=124.56  Aligned_cols=82  Identities=13%  Similarity=0.111  Sum_probs=75.7

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +..++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.+ +..+.|+.|.|.++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            34578999999999999999999999999998888888888999999999999999999999887 58999999999998


Q ss_pred             cCC
Q psy15852        261 TPK  263 (661)
Q Consensus       261 ~~k  263 (661)
                      ..+
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            754

>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=99.52  E-value=2.5e-14  Score=123.69  Aligned_cols=79  Identities=20%  Similarity=0.429  Sum_probs=74.1

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.+. +++++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            345899999999999999999999999999999999998 8999999999999999999999975 78999999999998


Q ss_pred             c
Q psy15852        261 T  261 (661)
Q Consensus       261 ~  261 (661)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=1.2e-14  Score=128.51  Aligned_cols=64  Identities=22%  Similarity=0.246  Sum_probs=58.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCe----eEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEI----ENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I----~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      ...+|||+||||++|++||+++|++||.|    .+|+|++|+ +|+++|||||+|.+.++|.+||.+..
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~~~   89 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRKHK   89 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTTTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCC
Confidence            35799999999999999999999999985    699999995 79999999999999999999999733

>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=99.52  E-value=6.8e-14  Score=121.20  Aligned_cols=77  Identities=17%  Similarity=0.318  Sum_probs=70.5

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC-----eEEE
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND-----KEVD  256 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g-----~~i~  256 (661)
                      ..++|||+|||+++++++|+++|++||+|..|.|+.+       |||||+|.+.++|++||+.+ +..|.|     +.|.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~   86 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   86 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEE
Confidence            4589999999999999999999999999999999875       89999999999999999987 578899     9999


Q ss_pred             EEeccCCCCC
Q psy15852        257 VKKATPKPEP  266 (661)
Q Consensus       257 V~~a~~k~~~  266 (661)
                      |.++.++...
T Consensus        87 V~~a~~~~~~   96 (108)
T 1x4c_A           87 VKVDGPRSPS   96 (108)
T ss_dssp             EEESSCCSCC
T ss_pred             EEeCCCCCCC
Confidence            9999986643

>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=99.51  E-value=2e-14  Score=125.30  Aligned_cols=83  Identities=18%  Similarity=0.298  Sum_probs=75.2

Q ss_pred             cCCeeEecCCCccCCHHHHH---HHHhcCCCeEEEEeccCCCCC---CcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEE
Q psy15852        183 KSGKIFVGGLSPEMKDEEIK---AHFAQFGNIIETEMPYDKSKS---QRKNFCFITFEHESVVIDLLKNP-KQKINDKEV  255 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~---~~F~~~G~i~~v~i~~~~~~g---~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i  255 (661)
                      ..++|||+|||+++++++|+   ++|++||+|..|.|+++..++   .++|||||+|.+.++|++|++.+ +..++|++|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l   93 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   93 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEE
Confidence            35799999999999999999   999999999999999887654   55699999999999999999985 688999999


Q ss_pred             EEEeccCCCC
Q psy15852        256 DVKKATPKPE  265 (661)
Q Consensus       256 ~V~~a~~k~~  265 (661)
                      .|.++.++..
T Consensus        94 ~V~~a~~k~~  103 (111)
T 2cpi_A           94 KASLGTTKYC  103 (111)
T ss_dssp             EEESCCCCSC
T ss_pred             EEEecccccc
Confidence            9999998763

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

Probab=99.51  E-value=3.2e-14  Score=123.04  Aligned_cols=79  Identities=14%  Similarity=0.219  Sum_probs=72.9

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK  263 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k  263 (661)
                      .++|||+|||+++++++|+++|++| .|.+|.|++++. |+++|||||+|.+.++|++||+.++..|+||.|.|..+.++
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECCHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCcc
Confidence            3689999999999999999999999 899999999876 99999999999999999999976678999999999988764


Q ss_pred             C
Q psy15852        264 P  264 (661)
Q Consensus       264 ~  264 (661)
                      .
T Consensus        94 ~   94 (109)
T 2dnn_A           94 Q   94 (109)
T ss_dssp             H
T ss_pred             c
Confidence            3

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

Probab=99.51  E-value=3.5e-14  Score=121.14  Aligned_cols=82  Identities=18%  Similarity=0.330  Sum_probs=73.8

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ...++++.++++++++++|+++|++||+|.+|+|+.++ +++++|||||+|.+.++|++|    +..+++..+.|+.|.|
T Consensus        16 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~v   90 (100)
T 2do4_A           16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQA----VMKMDGMTIKENIIKV   90 (100)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHH----HHHHTTEESSSCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHH----HHHhCCCEECCEEEEE
Confidence            34566666666699999999999999999999999998 799999999999999999999    8899999999999999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .++.++.
T Consensus        91 ~~a~~~~   97 (100)
T 2do4_A           91 AISNSGP   97 (100)
T ss_dssp             EECCCCS
T ss_pred             EECCCCC
Confidence            9987654

>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=99.51  E-value=1.7e-14  Score=126.26  Aligned_cols=62  Identities=16%  Similarity=0.101  Sum_probs=59.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCe-eEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEI-ENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I-~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      ..++|||+|||+++|+++|+++|++||.| .+|+|++|+ ||+++|||||+|.+.++|.+||+.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~   76 (114)
T 2cpy_A           14 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL   76 (114)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG
T ss_pred             CccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh
Confidence            35799999999999999999999999999 899999998 899999999999999999999988

>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=99.51  E-value=2.7e-14  Score=125.27  Aligned_cols=83  Identities=16%  Similarity=0.238  Sum_probs=75.0

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ...+++|.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..|.|+.|.|
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~V   99 (115)
T 2cpz_A           24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA----IQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHH----HHHHTTCEETTEECEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHH----HHHcCCCEECCEEEEE
Confidence            345566666666999999999999999999999999998999999999999999999999    8899999999999999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .++.++.
T Consensus       100 ~~a~~~~  106 (115)
T 2cpz_A          100 QLKRSKN  106 (115)
T ss_dssp             ECCCCSC
T ss_pred             EEcCCCC
Confidence            9987654

>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=99.51  E-value=3.4e-14  Score=118.42  Aligned_cols=79  Identities=25%  Similarity=0.437  Sum_probs=71.5

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    + .+++..+.|+.|.|.+
T Consensus         7 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a----~-~~~g~~~~g~~l~V~~   81 (89)
T 3ucg_A            7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS----L-ALDESLFRGRQIKVIP   81 (89)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHH----G-GGTTCEETTEECEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHH----H-hcCCCEECCcEEEEEE
Confidence            4555555556999999999999999999999999998999999999999999999998    7 9999999999999998


Q ss_pred             hhcc
Q psy15852        180 AKAK  183 (661)
Q Consensus       180 ~~~~  183 (661)
                      +++.
T Consensus        82 a~~~   85 (89)
T 3ucg_A           82 KRTN   85 (89)
T ss_dssp             TTTT
T ss_pred             ccCC
Confidence            8764

>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=99.51  E-value=8.5e-15  Score=123.73  Aligned_cols=81  Identities=14%  Similarity=0.135  Sum_probs=73.6

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +..++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.+ +..+.|++|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            44589999999999999999999999999999999988888999999999999999999999975 78999999999987


Q ss_pred             cC
Q psy15852        261 TP  262 (661)
Q Consensus       261 ~~  262 (661)
                      .+
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            63

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

Probab=99.51  E-value=1.7e-14  Score=123.61  Aligned_cols=83  Identities=22%  Similarity=0.288  Sum_probs=75.0

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ...++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..|.|+.|.|
T Consensus        11 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l~V   86 (102)
T 2cqb_A           11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA----IDNMNESELFGRTIRV   86 (102)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHH----HHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHH----HHHhCCCEECCcEEEE
Confidence            345666666666999999999999999999999999999999999999999999999999    8899999999999999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .++.++.
T Consensus        87 ~~a~~~~   93 (102)
T 2cqb_A           87 NLAKPMR   93 (102)
T ss_dssp             EECCCCC
T ss_pred             EeCCCCC
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=99.51  E-value=3.7e-14  Score=120.70  Aligned_cols=77  Identities=12%  Similarity=0.051  Sum_probs=69.3

Q ss_pred             cCCeeEecCCCc-cCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC---CCccCCeEEEEE
Q psy15852        183 KSGKIFVGGLSP-EMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP---KQKINDKEVDVK  258 (661)
Q Consensus       183 ~~~~lfV~nLp~-~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~---~~~~~g~~i~V~  258 (661)
                      +.++|||+|||+ .+++++|+++|++||.|.+|.|+++      +|||||+|.+.++|.+|++.+   ...+.|++|.|.
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   87 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   87 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEE
Confidence            457899999999 9999999999999999999999864      689999999999999999976   246999999999


Q ss_pred             eccCCCC
Q psy15852        259 KATPKPE  265 (661)
Q Consensus       259 ~a~~k~~  265 (661)
                      ++..+..
T Consensus        88 ~a~~~~~   94 (102)
T 1x4d_A           88 LSQKYKR   94 (102)
T ss_dssp             EECCCTT
T ss_pred             ECCCCCC
Confidence            9987553

>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=99.51  E-value=4.3e-14  Score=123.50  Aligned_cols=79  Identities=16%  Similarity=0.199  Sum_probs=71.8

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC---CCccCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP---KQKINDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~---~~~~~g~~i~V~  258 (661)
                      ++.++|||+|||+++++++|+++|++||.|.+|.|+++      +|||||+|.+.++|.+|++.+   +..+.|++|.|.
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            44689999999999999999999999999999999864      799999999999999999976   367999999999


Q ss_pred             eccCCCCC
Q psy15852        259 KATPKPEP  266 (661)
Q Consensus       259 ~a~~k~~~  266 (661)
                      ++.++...
T Consensus       103 ~a~~k~~~  110 (119)
T 2ad9_A          103 FSNHKELK  110 (119)
T ss_dssp             ECSSSSCC
T ss_pred             EccCCCCC
Confidence            99887654

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

Probab=99.51  E-value=2e-14  Score=123.36  Aligned_cols=81  Identities=22%  Similarity=0.401  Sum_probs=73.2

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|+.++.+++++|||||+|.+.++|++|    +..+++..|.|+.|.|.
T Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A           13 MITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA----EAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHH----HHHHSSCCBTTBCCEEE
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHH----HHHcCCCEECCcEEEEE
Confidence            44555555555999999999999999999999999999999999999999999999999    88899999999999999


Q ss_pred             hhhcc
Q psy15852        179 KAKAK  183 (661)
Q Consensus       179 ~~~~~  183 (661)
                      ++.+.
T Consensus        89 ~a~~~   93 (103)
T 2dnm_A           89 VARYG   93 (103)
T ss_dssp             ECSSC
T ss_pred             ECCcC
Confidence            98754

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.26  E-value=1.4e-15  Score=133.82  Aligned_cols=84  Identities=19%  Similarity=0.289  Sum_probs=77.8

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEE--------EEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIE--------TEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND  252 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~--------v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g  252 (661)
                      +..++|||+|||..+++++|+++|++||.|..        |.++.++.+++++|||||+|.+.++|.+|++.+ +..+.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            34578999999999999999999999999999        999999888999999999999999999999976 688999


Q ss_pred             eEEEEEeccCCCC
Q psy15852        253 KEVDVKKATPKPE  265 (661)
Q Consensus       253 ~~i~V~~a~~k~~  265 (661)
                      +.|.|.++.++..
T Consensus        85 ~~l~V~~a~~~~~   97 (116)
T 2lcw_A           85 NPIKVSFATRRAD   97 (116)
Confidence            9999999988764

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=3.7e-14  Score=122.21  Aligned_cols=80  Identities=26%  Similarity=0.510  Sum_probs=71.3

Q ss_pred             CcEEEEcCC-CcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGI-VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~-~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+.||++|+ +++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +.. ++..|.|+.|.|.
T Consensus        16 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a----~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           16 IGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV----LAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             SSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHH----HHH-CSEEETTEEEBCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHH----HHh-CCCeECCEEEEEE
Confidence            444555555 5999999999999999999999999999999999999999999999998    777 9999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        91 ~a~~~~   96 (105)
T 2dh8_A           91 PCTPRG   96 (105)
T ss_dssp             CSCCSS
T ss_pred             EccCCC
Confidence            987654

>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=99.51  E-value=6.8e-14  Score=119.15  Aligned_cols=79  Identities=19%  Similarity=0.268  Sum_probs=71.2

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC---CCccCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP---KQKINDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~---~~~~~g~~i~V~  258 (661)
                      ++.++|||+|||+.+++++|+++|++||.|.+|.++++      +|||||+|.+.++|.+|++.+   +..+.|++|.|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   86 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   86 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEE
Confidence            45689999999999999999999999999999998764      899999999999999999864   468999999999


Q ss_pred             eccCCCCC
Q psy15852        259 KATPKPEP  266 (661)
Q Consensus       259 ~a~~k~~~  266 (661)
                      ++.++...
T Consensus        87 ~a~~~~~~   94 (101)
T 2cq1_A           87 YSNHKELK   94 (101)
T ss_dssp             ECSCSSCC
T ss_pred             EcCcccCc
Confidence            99887654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=6.9e-14  Score=119.55  Aligned_cols=80  Identities=19%  Similarity=0.362  Sum_probs=71.3

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+++++++|+++|++||.|   .++.+ .+++++|||||+|.+.++|++|++.+ +..+.|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   88 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ   88 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEc
Confidence            345899999999999999999999999987   56665 56899999999999999999999976 67899999999999


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .++..
T Consensus        89 ~~~~~   93 (101)
T 2fc9_A           89 GPRGS   93 (101)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            88654

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

Probab=99.50  E-value=3.9e-14  Score=124.23  Aligned_cols=81  Identities=23%  Similarity=0.388  Sum_probs=72.8

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .+|+|.++++++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..|.|+.|.|.+
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA----IQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH----HHHTTTCEETTEECEEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHH----HHHhCCCEECCEEEEEEE
Confidence            3455555555999999999999999999999999988999999999999999999999    889999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        92 a~~~~   96 (115)
T 2dgo_A           92 ATRKP   96 (115)
T ss_dssp             SSCCC
T ss_pred             ccCCC
Confidence            87654

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

Probab=99.50  E-value=1.1e-14  Score=131.00  Aligned_cols=82  Identities=20%  Similarity=0.293  Sum_probs=75.8

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEE--EEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CC----ccCCeEE
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIE--TEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQ----KINDKEV  255 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~--v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~----~~~g~~i  255 (661)
                      ..++|||+|||+++++++|+++|++||.|..  |+|++++.+++++|||||+|.+. +|.+|+..+ +.    .++|+.|
T Consensus        22 ~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l  100 (131)
T 2m2b_A           22 ANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTI  100 (131)
T ss_dssp             CCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEE
Confidence            3479999999999999999999999999977  99999999999999999999999 999999987 56    8999999


Q ss_pred             EEEeccCCCC
Q psy15852        256 DVKKATPKPE  265 (661)
Q Consensus       256 ~V~~a~~k~~  265 (661)
                      .|.++.++..
T Consensus       101 ~V~~a~~~~~  110 (131)
T 2m2b_A          101 NVEFAKGSKR  110 (131)
T ss_dssp             CCEECCCSCC
T ss_pred             EEEECCCCCC
Confidence            9999987653

>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=99.50  E-value=5.5e-15  Score=123.56  Aligned_cols=80  Identities=28%  Similarity=0.553  Sum_probs=72.0

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ++|||+|||.++++++|+++|++||+|.+|.+++++.++.++|||||+|.+.+ |.+|+..+ +..++|+.|.|.++.++
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            57999999999999999999999999999999999999999999999999999 99999987 68899999999999886


Q ss_pred             CC
Q psy15852        264 PE  265 (661)
Q Consensus       264 ~~  265 (661)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>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=99.50  E-value=3.8e-14  Score=123.39  Aligned_cols=83  Identities=19%  Similarity=0.335  Sum_probs=75.2

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhC------Ceeec
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEG------NHVIN  171 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~------~~~i~  171 (661)
                      ...++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..++      +..|.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A----~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           14 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC----LAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHH----HHHHCTTTTTCCEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHH----HHHhccccccCCcEEc
Confidence            345666666666999999999999999999999999999999999999999999999999    88899      99999


Q ss_pred             ceeehhhhhhccC
Q psy15852        172 NKKIEAKKAKAKS  184 (661)
Q Consensus       172 g~~i~v~~~~~~~  184 (661)
                      |+.|.|.++.++.
T Consensus        90 g~~l~v~~a~~~~  102 (111)
T 1x4h_A           90 GRQLKVDLAVTRD  102 (111)
T ss_dssp             SCEEEEECCCCCC
T ss_pred             CEEEEEEECCCCc
Confidence            9999999987654

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

Probab=99.50  E-value=3.2e-14  Score=122.83  Aligned_cols=81  Identities=17%  Similarity=0.315  Sum_probs=72.4

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+|+|+.++.+|+++|||||+|.+.++|++|    +..+++..+.|+.|.|.+
T Consensus        24 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA----MEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHH----HHHHTTCBSSSSBCEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHH----HHHhcCCEECCcEEEEEe
Confidence            3444444445999999999999999999999999999999999999999999999999    888999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            87653

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

Probab=99.50  E-value=3.1e-14  Score=121.01  Aligned_cols=83  Identities=25%  Similarity=0.366  Sum_probs=73.9

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCC---CCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeeccee
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPN---TGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK  174 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~---tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~  174 (661)
                      +..++++.++++++++++|+++|++||+|.+|+|++++.   |++++|||||+|.+.++|++|    +..+++..|.|+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~   79 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA----LKQLQGHTVDGHK   79 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHH----HHHSTTCEETTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHH----HHHhCCCeeCCeE
Confidence            345666666666999999999999999999999999876   669999999999999999999    8889999999999


Q ss_pred             ehhhhhhccC
Q psy15852        175 IEAKKAKAKS  184 (661)
Q Consensus       175 i~v~~~~~~~  184 (661)
                      |.|.++.++.
T Consensus        80 l~V~~a~~~~   89 (98)
T 2cpf_A           80 LEVRISERAT   89 (98)
T ss_dssp             CEEECSSCSS
T ss_pred             EEEEEccCCC
Confidence            9999987654

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

Probab=99.50  E-value=2.7e-14  Score=116.01  Aligned_cols=73  Identities=5%  Similarity=0.121  Sum_probs=67.7

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      .+..|||+||++.+|+++|+++|.+||+|.++++..      ++|||||+|.++++|.+|++.+ +..+.|++|.|++|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            356799999999999999999999999999999954      5999999999999999999997 579999999999985

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

Probab=99.50  E-value=2e-14  Score=121.71  Aligned_cols=82  Identities=26%  Similarity=0.340  Sum_probs=73.4

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEE-EEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENV-TLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v-~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ..++++.++++++++++|+++|++||+|.+| +|++++.+++++|||||+|.+.++|++|    +..+++..+.|++|.|
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l~v   80 (96)
T 1x5t_A            5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA----IEAMNGQYLCNRPITV   80 (96)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHH----HHTTTTCEETTEECEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHH----HHHcCCCEECCEEEEE
Confidence            3455555555599999999999999999999 9999988999999999999999999999    8889999999999999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .++.++.
T Consensus        81 ~~a~~~~   87 (96)
T 1x5t_A           81 SYAFKKD   87 (96)
T ss_dssp             EESCCCC
T ss_pred             EEecccC
Confidence            9987654

>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=99.50  E-value=3e-14  Score=123.41  Aligned_cols=82  Identities=23%  Similarity=0.430  Sum_probs=73.3

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|++++.+|+++|||||+|.+.++|++|    +..+++..+.|++|.|.
T Consensus        26 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A----i~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           26 PMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA----LEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             CEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHH----HHHHTTCCSSSSCCEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHH----HHHcCCCEECCEEEEEE
Confidence            34455555555999999999999999999999999999999999999999999999999    88999999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            887653

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

Probab=99.50  E-value=1.5e-14  Score=130.67  Aligned_cols=66  Identities=27%  Similarity=0.350  Sum_probs=62.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      .++|||+|||+++|+++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|++|++.++..
T Consensus        47 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~  112 (135)
T 2lea_A           47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGA  112 (135)
T ss_dssp             CCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC
Confidence            578999999999999999999999999999999999999999999999999999999999976643

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

Probab=99.50  E-value=7.3e-14  Score=116.68  Aligned_cols=77  Identities=26%  Similarity=0.557  Sum_probs=70.2

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +..++|||+|||.++++++|+++|++||.|..|.++        +|||||+|.+.++|.+|++.+ +..++|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            345799999999999999999999999999999996        689999999999999999876 67899999999999


Q ss_pred             cCCCCC
Q psy15852        261 TPKPEP  266 (661)
Q Consensus       261 ~~k~~~  266 (661)
                      .++...
T Consensus        78 ~~~~~~   83 (90)
T 2dnq_A           78 KNKSKA   83 (90)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            887653

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

Probab=99.49  E-value=3.3e-14  Score=121.07  Aligned_cols=78  Identities=23%  Similarity=0.315  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCC-cCCHHHHHHHhhcCCCeeE--------EEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCee
Q psy15852         99 KNKMVSHPGIV-HKITEELKEHFSKYGEIEN--------VTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV  169 (661)
Q Consensus        99 ~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~--------v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~  169 (661)
                      ..+.+|++|+| ++++++|+++|++||.|.+        |+|++++.+|+++|||||+|.+.++|++|    +..+++..
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~A----i~~l~g~~   87 (99)
T 2la6_A           12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAA----IDWFDGKE   87 (99)
T ss_dssp             CCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHH----HHHHTTCB
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHH----HHHhCCCE
Confidence            34455555555 9999999999999999999        99999999999999999999999999999    88899999


Q ss_pred             ecceeehhhhh
Q psy15852        170 INNKKIEAKKA  180 (661)
Q Consensus       170 i~g~~i~v~~~  180 (661)
                      +.|+.|.|.++
T Consensus        88 ~~g~~l~V~~A   98 (99)
T 2la6_A           88 FSGNPIKVSFA   98 (99)
T ss_dssp             SSSSBCEEEEC
T ss_pred             eCCcEEEEEec
Confidence            99999998875

>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=1.8e-14  Score=127.58  Aligned_cols=80  Identities=21%  Similarity=0.380  Sum_probs=73.7

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeE--EEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNII--ETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      ..++|||+|||+++++++|+++|++| .|.  +|.|++++. |+++|||||+|.+.++|++||+.++..|+||.|.|.++
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~a  118 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKS  118 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEEC
Confidence            45789999999999999999999999 677  999999987 99999999999999999999998889999999999988


Q ss_pred             cCCC
Q psy15852        261 TPKP  264 (661)
Q Consensus       261 ~~k~  264 (661)
                      .++.
T Consensus       119 ~~~e  122 (126)
T 2hgm_A          119 SQEE  122 (126)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            7543

>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=99.49  E-value=2.5e-14  Score=128.79  Aligned_cols=64  Identities=14%  Similarity=0.054  Sum_probs=60.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCC---eeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGE---IENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~---I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      .++|||+|||+++||+||+++|++||.   |.+|+|++|+. |+++|||||+|.+.++|++|++ ++..
T Consensus        44 ~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~  110 (136)
T 2hgl_A           44 GFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRE  110 (136)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCC
Confidence            578999999999999999999999999   89999999988 9999999999999999999999 6543

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

Probab=99.49  E-value=2e-14  Score=123.12  Aligned_cols=82  Identities=28%  Similarity=0.495  Sum_probs=73.5

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|    +..+++..|.|++|.|.
T Consensus        12 ~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A           12 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA----MMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHH----HHHHTTCCTTSCCCEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHH----HHHhCCCEECCeEEEEE
Confidence            34455555555999999999999999999999999998999999999999999999999    88999999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        88 ~a~~~~   93 (102)
T 1x5s_A           88 QAGKSS   93 (102)
T ss_dssp             EEECCC
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=99.49  E-value=1.1e-13  Score=118.53  Aligned_cols=79  Identities=18%  Similarity=0.188  Sum_probs=70.5

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC---CCccCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP---KQKINDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~---~~~~~g~~i~V~  258 (661)
                      ++.++|||+|||+.+++++|+++|++||.|.+|.++++      +|||||+|.+.++|.+|++.+   ...+.|++|.|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            34589999999999999999999999999999998753      799999999999999999875   356999999999


Q ss_pred             eccCCCCC
Q psy15852        259 KATPKPEP  266 (661)
Q Consensus       259 ~a~~k~~~  266 (661)
                      ++..+...
T Consensus        87 ~a~~~~~~   94 (104)
T 1wex_A           87 YSTSKRIT   94 (104)
T ss_dssp             ECSSSSCC
T ss_pred             EccCcccc
Confidence            99886643

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

Probab=99.49  E-value=2.4e-13  Score=128.54  Aligned_cols=67  Identities=21%  Similarity=0.263  Sum_probs=62.8

Q ss_pred             cCCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        591 EAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       591 ~~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ...++|||.|||+++++++|+++|++||.|.+|+|+.++ +|+++|||||+|.+.++|.+|++.++..
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~  152 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGV  152 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCC
Confidence            346899999999999999999999999999999999998 8999999999999999999999977654

>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=4e-14  Score=125.33  Aligned_cols=62  Identities=31%  Similarity=0.332  Sum_probs=58.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCee--EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIE--NVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~--~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      .++|||+|||+++||+||+++|++| .|+  +|+|++|+. |+++|||||+|.+.++|.+||+...
T Consensus        42 ~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~  105 (126)
T 2hgm_A           42 DGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHK  105 (126)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCC
Confidence            5789999999999999999999999 677  999999988 9999999999999999999998643

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

Probab=99.49  E-value=2e-14  Score=118.76  Aligned_cols=80  Identities=16%  Similarity=0.235  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      +..++++.++++++++++|+++|++||+|.+|+|+.++.+++++|||||+|.+.++|++|    +..+|+..+.|+.+++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~~~~   79 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA----VTALKASGVQAQMAKQ   79 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHH----HHHHHHHTCCEESCCS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHH----HHHhcCCeEeeEEEee
Confidence            344555655556999999999999999999999999999999999999999999999999    8889999999999998


Q ss_pred             hhhh
Q psy15852        178 KKAK  181 (661)
Q Consensus       178 ~~~~  181 (661)
                      .++.
T Consensus        80 ~~~~   83 (85)
T 1x4e_A           80 SGPS   83 (85)
T ss_dssp             SCCC
T ss_pred             cCCC
Confidence            7654

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

Probab=99.49  E-value=4.3e-14  Score=122.20  Aligned_cols=60  Identities=17%  Similarity=0.264  Sum_probs=56.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      ..+|||+|||+++||+||+++|++| .|.+|+|++|+. |+++|||||+|.+.++|.+||..
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~~   75 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKR   75 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhc
Confidence            4689999999999999999999999 899999999986 99999999999999999999954

>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=99.49  E-value=2.8e-14  Score=123.43  Aligned_cols=65  Identities=15%  Similarity=0.141  Sum_probs=60.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCC---eeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGE---IENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~---I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ...+|||+|||+++|++||+++|+.||.   |.+|+|++|+. |+++|||||+|.+.++|.+||+ +|..
T Consensus        10 ~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~   77 (107)
T 2lmi_A           10 DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRM   77 (107)
T ss_dssp             SCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcc
Confidence            4679999999999999999999999998   99999999988 9999999999999999999999 5543

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

Probab=99.49  E-value=4.2e-14  Score=130.81  Aligned_cols=79  Identities=16%  Similarity=0.276  Sum_probs=71.8

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCC--CeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYG--EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G--~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      .+++|.+|++++++++|+++|++||  .|.+|+|++|+.+|++||||||+|.+.++|++|    +..+++..|.|+.|.|
T Consensus        56 ~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~A----i~~lng~~~~Gr~l~V  131 (156)
T 3n9u_C           56 AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKL----LELLPGKVLNGEKVDV  131 (156)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHH----HHHSTTCEETTEECEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHH----HHHcCCCEECCeEeEE
Confidence            4555555555999999999999999  999999999999999999999999999999999    8999999999999999


Q ss_pred             hhhhc
Q psy15852        178 KKAKA  182 (661)
Q Consensus       178 ~~~~~  182 (661)
                      .++.+
T Consensus       132 ~~a~~  136 (156)
T 3n9u_C          132 RPATR  136 (156)
T ss_dssp             EECCH
T ss_pred             EEcCC
Confidence            88764

>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=99.49  E-value=6e-14  Score=118.45  Aligned_cols=78  Identities=22%  Similarity=0.301  Sum_probs=69.7

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|++++. ++++|||||+|.+.++|++|    +..+++..+.|++|.|.
T Consensus        16 ~~~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           16 DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYA----IALLNGIRLYGRPINVS   90 (95)
T ss_dssp             GGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHH----HHHhCCCEECCCEEEEE
Confidence            34455555555999999999999999999999999986 99999999999999999999    88899999999999998


Q ss_pred             hhh
Q psy15852        179 KAK  181 (661)
Q Consensus       179 ~~~  181 (661)
                      +++
T Consensus        91 ~a~   93 (95)
T 2ywk_A           91 GPS   93 (95)
T ss_dssp             CCC
T ss_pred             EcC
Confidence            875

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.49  E-value=3.9e-14  Score=124.78  Aligned_cols=64  Identities=14%  Similarity=0.108  Sum_probs=60.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCC---eeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGE---IENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~---I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      ..++|||+|||+++|++||+++|++||.   |.+|+|++++. |+++|||||+|.+.++|.+||+ +|.
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g   82 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDR   82 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCC
Confidence            4678999999999999999999999999   89999999987 9999999999999999999999 554

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

Probab=99.49  E-value=2.3e-14  Score=125.48  Aligned_cols=64  Identities=17%  Similarity=0.311  Sum_probs=60.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCC---CCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNT---GRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~t---g~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      ..++|||+|||+++|+++|+++|++||.|. +.++.++.|   |+++|||||+|.+.++|.+||+.++
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~   73 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL   73 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh
Confidence            357899999999999999999999999999 999999887   8999999999999999999999764

>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=99.49  E-value=3.9e-14  Score=126.76  Aligned_cols=83  Identities=25%  Similarity=0.420  Sum_probs=75.1

Q ss_pred             cCCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852         97 EAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus        97 ~~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ++..+++|.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..|.|++|.
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~A----i~~lng~~i~g~~l~  119 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA----KERANGMELDGRRIR  119 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHH----HHHHTTCCSSSSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHH----HHHhCCCEECCEEEE
Confidence            3455666666666999999999999999999999999999999999999999999999999    888999999999999


Q ss_pred             hhhhhcc
Q psy15852        177 AKKAKAK  183 (661)
Q Consensus       177 v~~~~~~  183 (661)
                      |.++.++
T Consensus       120 V~~a~~~  126 (129)
T 2kxn_B          120 VDFSITK  126 (129)
T ss_dssp             ESCCSSS
T ss_pred             EEEecCC
Confidence            9998764

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

Probab=99.49  E-value=5.9e-14  Score=119.98  Aligned_cols=76  Identities=22%  Similarity=0.376  Sum_probs=70.7

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ++|||+|||+++++++|+++|++||+|..|.++.+     ++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++.++
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            47999999999999999999999999999999876     6899999999999999999976 68899999999999887


Q ss_pred             CC
Q psy15852        264 PE  265 (661)
Q Consensus       264 ~~  265 (661)
                      ..
T Consensus        76 ~~   77 (101)
T 2hvz_A           76 PR   77 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.48  E-value=5.3e-14  Score=122.07  Aligned_cols=65  Identities=22%  Similarity=0.263  Sum_probs=61.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCC-eeEEEEe-ecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGE-IENVTLK-SDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~-I~~v~i~-~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      ..++|||+|||+++|+++|+++|++||. |.+|+|+ .++.||+++|||||+|.+.++|.+|++.++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~   73 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLM   73 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhh
Confidence            3579999999999999999999999998 9999999 888899999999999999999999999875

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

Probab=99.48  E-value=5.3e-14  Score=123.96  Aligned_cols=78  Identities=18%  Similarity=0.277  Sum_probs=69.6

Q ss_pred             CcEEEEcCC-CcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGI-VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~-~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+.||++|+ +++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..+.|+.|.|.
T Consensus        40 ~~~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           40 GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA----IKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             SEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHH----HHHCCCCEETTEECCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHH----HHHcCCCEECCEEEEEE
Confidence            344555555 5999999999999999999999999998999999999999999999999    88999999999999998


Q ss_pred             hhh
Q psy15852        179 KAK  181 (661)
Q Consensus       179 ~~~  181 (661)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            753

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

Probab=99.48  E-value=5.4e-14  Score=121.58  Aligned_cols=83  Identities=24%  Similarity=0.390  Sum_probs=74.2

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeC-CCCCCcccEEEEEEeehhhHHHhhHHHHHHh-CCeeecceee
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSD-PNTGRSRGFAFIVFKDTESLEKASVEDVIAE-GNHVINNKKI  175 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~-~~tg~srG~afV~F~~~e~A~~A~~~~~~~~-~~~~i~g~~i  175 (661)
                      ...++++.++++++++++|+++|++||+|.+|+|+++ +.+++++|||||+|.+.++|++|    +..+ ++..|.|+.|
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A----~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA----FNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHH----HHHHHTCCBSSSCBC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHH----HHHhccCCeECCCEE
Confidence            3455666666669999999999999999999999998 77899999999999999999999    8889 9999999999


Q ss_pred             hhhhhhccC
Q psy15852        176 EAKKAKAKS  184 (661)
Q Consensus       176 ~v~~~~~~~  184 (661)
                      .|.++.++.
T Consensus        90 ~v~~a~~~~   98 (107)
T 2cph_A           90 VLEWADSEV   98 (107)
T ss_dssp             EEEECCCCC
T ss_pred             EEEeCCCCC
Confidence            999987654

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

Probab=99.48  E-value=7.2e-14  Score=119.67  Aligned_cols=81  Identities=26%  Similarity=0.386  Sum_probs=72.7

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||.++++++|+++|++|+   .|.++.++.++.++|||||+|.+.++|.+||+.+ +..|.|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA   89 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            3458999999999999999999999874   5777778888999999999999999999999975 78999999999999


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .++..
T Consensus        90 ~~~~~   94 (102)
T 2fc8_A           90 KPKGE   94 (102)
T ss_dssp             CCCCS
T ss_pred             cCCCC
Confidence            98764

>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=99.48  E-value=1.1e-13  Score=121.00  Aligned_cols=66  Identities=18%  Similarity=0.202  Sum_probs=62.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|++++ +|+++|||||+|.+.++|.+|++.+|..
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~   89 (114)
T 1x5o_A           24 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGK   89 (114)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            45899999999999999999999999999999999998 8999999999999999999999976653

>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=99.48  E-value=5.6e-14  Score=122.18  Aligned_cols=81  Identities=25%  Similarity=0.327  Sum_probs=72.4

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+|+|+.++.+|+++|||||+|.+.++|++|    +..+++..+.|+.|.|.+
T Consensus        27 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A----i~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           27 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA----KEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHH----HHHHTTCEETTEECEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHH----HHHcCCCEECCcEEEEEE
Confidence            3444444455999999999999999999999999998999999999999999999999    888999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus       103 a~~~~  107 (110)
T 1oo0_B          103 CFVKG  107 (110)
T ss_dssp             SEESS
T ss_pred             cccCC
Confidence            87653

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

Probab=99.48  E-value=5.3e-14  Score=122.08  Aligned_cols=80  Identities=21%  Similarity=0.484  Sum_probs=73.3

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||.++++++|+++|++||.|..|.++.+.  +.++|||||+|.+.++|.+|++.+ +..++|+.|.|.++.
T Consensus        28 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  105 (109)
T 2err_A           28 QPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT  105 (109)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            35899999999999999999999999999999999886  458999999999999999999975 789999999999998


Q ss_pred             CCC
Q psy15852        262 PKP  264 (661)
Q Consensus       262 ~k~  264 (661)
                      ++.
T Consensus       106 ~~~  108 (109)
T 2err_A          106 ARV  108 (109)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            753

>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=99.48  E-value=4.1e-14  Score=125.86  Aligned_cols=67  Identities=15%  Similarity=0.176  Sum_probs=61.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCccc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY  659 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~~  659 (661)
                      ...+|||+|||+++|+++|+++|++||.|.+|.++.+..||+++|||||+|.+.++|.+||+ +|..+
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~   90 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQY   90 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCe
Confidence            45799999999999999999999999999998888888899999999999999999999999 66543

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

Probab=99.48  E-value=6.4e-14  Score=120.23  Aligned_cols=80  Identities=16%  Similarity=0.359  Sum_probs=71.1

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++|| |.+|+|++++.+++++|||||+|.+.++|++|    + .+++..|.|+.|.|.
T Consensus        15 ~~~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           15 PYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA----L-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHH----G-GGTTCEETTEECEEE
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHH----H-hhCCCeECCeEEEEE
Confidence            34455555555999999999999997 99999999999999999999999999999998    7 899999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        89 ~a~~~~   94 (103)
T 2dng_A           89 IAEGRK   94 (103)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            987654

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

Probab=99.48  E-value=7.3e-14  Score=124.25  Aligned_cols=82  Identities=18%  Similarity=0.398  Sum_probs=76.4

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||..+++++|+++|++||.|..|.++.++ +++++|||||+|.+.++|.+|++.+ +..++|+.|.|.++.
T Consensus        34 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  112 (124)
T 2kt5_A           34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  112 (124)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeC
Confidence            34799999999999999999999999999999999998 8999999999999999999999965 678999999999998


Q ss_pred             CCCC
Q psy15852        262 PKPE  265 (661)
Q Consensus       262 ~k~~  265 (661)
                      +...
T Consensus       113 ~~~~  116 (124)
T 2kt5_A          113 SQID  116 (124)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            8654

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

Probab=99.48  E-value=9.3e-14  Score=126.29  Aligned_cols=78  Identities=26%  Similarity=0.543  Sum_probs=73.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ..++|||+|||..+++++|+++|++||+|..|.+++++.+++++|||||+|.+.++|.+|++.+ +..+.|+.|.|.+|
T Consensus        62 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            4589999999999999999999999999999999999999999999999999999999999876 57899999999875

>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=99.48  E-value=6.3e-14  Score=122.67  Aligned_cols=79  Identities=22%  Similarity=0.346  Sum_probs=71.4

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .+++|.++++++++++|+++|++||.|.+|+|+.++.+++++|||||+|.+.++|++|    + .+++..|.|+.|.|.+
T Consensus        26 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A----~-~l~g~~~~g~~l~V~~  100 (114)
T 2cq4_A           26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA----I-GLTGQRLLGVPIIVQA  100 (114)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHH----H-HHTTEEETTEEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHH----H-HcCCCEeCCeEEEEEe
Confidence            4555555555999999999999999999999999999999999999999999999998    8 9999999999999998


Q ss_pred             hhcc
Q psy15852        180 AKAK  183 (661)
Q Consensus       180 ~~~~  183 (661)
                      +.++
T Consensus       101 a~~~  104 (114)
T 2cq4_A          101 SQAE  104 (114)
T ss_dssp             HHHH
T ss_pred             cCCC
Confidence            7654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=1.9e-14  Score=127.20  Aligned_cols=82  Identities=17%  Similarity=0.199  Sum_probs=74.3

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCe----EEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNI----IETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDV  257 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i----~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V  257 (661)
                      ...++|||+|||+++++++|+++|++||.|    ..|.|+.+. +|+++|||||+|.+.++|++||+.+++.+.||.|.|
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~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEE
Confidence            445899999999999999999999999975    689999884 799999999999999999999998788999999999


Q ss_pred             EeccCCC
Q psy15852        258 KKATPKP  264 (661)
Q Consensus       258 ~~a~~k~  264 (661)
                      ..+.++.
T Consensus       100 ~~a~~~e  106 (123)
T 2dha_A          100 FRSTAAE  106 (123)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9887544

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.48  E-value=3.8e-14  Score=124.85  Aligned_cols=82  Identities=15%  Similarity=0.233  Sum_probs=75.4

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCC---eEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGN---IIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~---i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~  258 (661)
                      ...++|||+|||+++++++|+++|++||.   |..|+|++++. ++++|||||+|.+.++|++||+..+..|+|+.|.|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~   93 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVF   93 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEE
Confidence            34578999999999999999999999999   89999999887 999999999999999999999966789999999999


Q ss_pred             eccCCC
Q psy15852        259 KATPKP  264 (661)
Q Consensus       259 ~a~~k~  264 (661)
                      ++..+.
T Consensus        94 ~a~~~~   99 (118)
T 2db1_A           94 KSHRTE   99 (118)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            987654

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

Probab=99.48  E-value=2e-13  Score=124.08  Aligned_cols=67  Identities=22%  Similarity=0.262  Sum_probs=63.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|.+|++.++..
T Consensus        62 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~  128 (140)
T 2ku7_A           62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES  128 (140)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEE
T ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCC
Confidence            4689999999999999999999999999999999999999999999999999999999999987653

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

Probab=99.47  E-value=8.5e-14  Score=119.66  Aligned_cols=82  Identities=22%  Similarity=0.263  Sum_probs=73.9

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhc-CCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCee-ecceee
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSK-YGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV-INNKKI  175 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~-~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~-i~g~~i  175 (661)
                      +..++++.++++++++++|+++|++ ||+|.+|+|++++ +++++|||||+|.+.++|.+|    +..+++.. +.|+.|
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A----~~~l~g~~~~~g~~l   82 (104)
T 2dhg_A            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRA----LTECQGAVGLGSKPV   82 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHH----HHHTTTCCSSSSSCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHH----HHHccCCcccCCEeE
Confidence            3456666666669999999999999 9999999999998 899999999999999999999    88899999 999999


Q ss_pred             hhhhhhccC
Q psy15852        176 EAKKAKAKS  184 (661)
Q Consensus       176 ~v~~~~~~~  184 (661)
                      .|.++.++.
T Consensus        83 ~v~~a~~~~   91 (104)
T 2dhg_A           83 RLSVAIPKA   91 (104)
T ss_dssp             CCCBCCCCC
T ss_pred             EEEEccCCC
Confidence            999987654

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

Probab=99.47  E-value=6.4e-14  Score=120.70  Aligned_cols=79  Identities=20%  Similarity=0.339  Sum_probs=72.5

Q ss_pred             CCeeEecCCCccC------CHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCe-EE
Q psy15852        184 SGKIFVGGLSPEM------KDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDK-EV  255 (661)
Q Consensus       184 ~~~lfV~nLp~~~------te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~-~i  255 (661)
                      .++|||+|||+.+      ++++|+++|++||.|.+|.|+  +.+|+++|||||+|.+.++|.+|++.+ +..+.|+ +|
T Consensus        15 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l   92 (105)
T 2nlw_A           15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   92 (105)
T ss_dssp             CSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEE
T ss_pred             CCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceE
Confidence            5799999999999      789999999999999999998  456899999999999999999999986 6789998 99


Q ss_pred             EEEeccCCC
Q psy15852        256 DVKKATPKP  264 (661)
Q Consensus       256 ~V~~a~~k~  264 (661)
                      .|.++....
T Consensus        93 ~V~~a~~~~  101 (105)
T 2nlw_A           93 RVNLFTDFD  101 (105)
T ss_dssp             EEECSCCCC
T ss_pred             EEEEcchHh
Confidence            999998654

>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=99.47  E-value=1.1e-13  Score=115.19  Aligned_cols=81  Identities=27%  Similarity=0.532  Sum_probs=64.0

Q ss_pred             hhhccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEE
Q psy15852        179 KAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVK  258 (661)
Q Consensus       179 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~  258 (661)
                      ...+...+|||+|||+++++++|+++|++||.|.+|.|+++     ++|||||+|.+.++|.++ ......+.|+.|.|.
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~-~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSL-CGEDLIIKGISVHIS   79 (89)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHH-TTCEEEETTEEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHH-cCCCcccCCEEEEEE
Confidence            34456689999999999999999999999999999999874     699999999999999853 222455779999999


Q ss_pred             eccCCCC
Q psy15852        259 KATPKPE  265 (661)
Q Consensus       259 ~a~~k~~  265 (661)
                      ++.++..
T Consensus        80 ~a~~k~~   86 (89)
T 3d2w_A           80 NAEPKHN   86 (89)
T ss_dssp             ECC----
T ss_pred             EcCCCCc
Confidence            9988654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.47  E-value=3.3e-14  Score=121.77  Aligned_cols=82  Identities=23%  Similarity=0.501  Sum_probs=75.7

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      ..++|||+|||+++++++|+++|++||.|..|.++.++ ++.++|||||+|.+.++|.+|++ .+..++|+.|.|.++.+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEEECCc
Confidence            45799999999999999999999999999999999998 89999999999999999999999 78899999999999987


Q ss_pred             CCCC
Q psy15852        263 KPEP  266 (661)
Q Consensus       263 k~~~  266 (661)
                      +...
T Consensus        86 ~~~~   89 (102)
T 2xs2_A           86 KQNL   89 (102)
T ss_dssp             CC--
T ss_pred             Ccch
Confidence            7643

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

Probab=99.47  E-value=7e-14  Score=117.86  Aligned_cols=60  Identities=18%  Similarity=0.179  Sum_probs=54.8

Q ss_pred             cCCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        591 EAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       591 ~~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      .+.++|||+|||+++|++||+++|++||.|.+|+|++      +||||||+|.+.++|.+|++.++
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln   78 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAA   78 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhc
Confidence            3467899999999999999999999999999999985      47899999999999999998654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=9.1e-14  Score=118.39  Aligned_cols=76  Identities=14%  Similarity=0.175  Sum_probs=65.5

Q ss_pred             CCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhC--Ceeecceee
Q psy15852         99 KNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEG--NHVINNKKI  175 (661)
Q Consensus        99 ~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~--~~~i~g~~i  175 (661)
                      ..+.|||+|+| ++++++|+++|++||+|.+|+|+++      ||||||+|.+.++|++|    +..++  +..|.|++|
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~A----i~~l~~~~~~l~Gr~l   84 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTM----VNYYTSVTPVLRGQPI   84 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHH----HHHHTTSCCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHH----HHHhccCCceECCEEE
Confidence            34556666665 9999999999999999999999974      68999999999999999    77765  578999999


Q ss_pred             hhhhhhccC
Q psy15852        176 EAKKAKAKS  184 (661)
Q Consensus       176 ~v~~~~~~~  184 (661)
                      .|.++.++.
T Consensus        85 ~V~~A~~~~   93 (105)
T 1sjq_A           85 YIQFSNHKE   93 (105)
T ss_dssp             CBCCCSSSS
T ss_pred             EEEEcCCCC
Confidence            999987654

>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=99.47  E-value=9.2e-14  Score=119.68  Aligned_cols=81  Identities=21%  Similarity=0.287  Sum_probs=71.6

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecc---eee
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN---KKI  175 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g---~~i  175 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|++++ +++++|||||+|.+.++|++|    +..+++..+.+   +.|
T Consensus        15 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A----i~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAA----IHALHGSQTMPGASSSL   89 (105)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHH----HHHHSSCCCCTTCSSCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHH----HHHHcCCccCCCCCccE
Confidence            3455555555599999999999999999999999988 699999999999999999999    88999999998   999


Q ss_pred             hhhhhhccC
Q psy15852        176 EAKKAKAKS  184 (661)
Q Consensus       176 ~v~~~~~~~  184 (661)
                      .|.++.++.
T Consensus        90 ~V~~a~~~~   98 (105)
T 2dnh_A           90 VVKFADTDK   98 (105)
T ss_dssp             EEEESCSSC
T ss_pred             EEEECccCc
Confidence            999887654

>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=99.47  E-value=2.7e-14  Score=128.93  Aligned_cols=62  Identities=18%  Similarity=0.144  Sum_probs=57.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      ..+|||+|||+++||+||+++|++|| |++|+|++|+. |+++|||||+|.+.++|++|| +++.
T Consensus        46 ~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g  107 (139)
T 2hgn_A           46 GHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDR  107 (139)
T ss_dssp             CCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCC
Confidence            57899999999999999999999999 77999999987 999999999999999999999 4443

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

Probab=99.46  E-value=2.6e-14  Score=122.26  Aligned_cols=84  Identities=26%  Similarity=0.363  Sum_probs=73.4

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      ++++.++++++++++|+++|++||+|.+|+|+++     ++|||||+|.+.++|++|    +..+++..+.|+.|.|.++
T Consensus         2 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~V~~a   72 (101)
T 2hvz_A            2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDA----VRGLDGKVICGSRVRVELS   72 (101)
T ss_dssp             EEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHH----HHHHHHSCSSSCCCEEEES
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHH----HHHHCCCeECCcEEEEEEc
Confidence            3455555559999999999999999999999986     789999999999999999    8889999999999999988


Q ss_pred             hccC---------------CeeEecCCC
Q psy15852        181 KAKS---------------GKIFVGGLS  193 (661)
Q Consensus       181 ~~~~---------------~~lfV~nLp  193 (661)
                      .++.               .+|||+||+
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           73 TGMPRRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             SSCCCSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             cCCCCcccCCCCCccccCCCceecCCCC
Confidence            6542               579999986

>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=99.46  E-value=6.4e-14  Score=123.00  Aligned_cols=81  Identities=31%  Similarity=0.385  Sum_probs=72.1

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..+++|.++++++++++|+++|++||+|.+|+|+.++ +++++|||||+|.+.++|++|    +..+++..+.|+.|.|.
T Consensus         7 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~A----i~~l~g~~~~g~~l~V~   81 (116)
T 2fy1_A            7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNA----AKDMNGKSLHGKAIKVE   81 (116)
T ss_dssp             CCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHH----HHHCSSCBCSSSBCEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHH----HHHhCCCEECCEEEEEE
Confidence            3455555555599999999999999999999999998 799999999999999999999    88999999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        82 ~a~~~~   87 (116)
T 2fy1_A           82 QAKKPS   87 (116)
T ss_dssp             ECCCSS
T ss_pred             ECCCCC
Confidence            887543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.46  E-value=5.8e-14  Score=114.80  Aligned_cols=71  Identities=21%  Similarity=0.401  Sum_probs=65.0

Q ss_pred             CeeEecCCCccC------CHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCe-EEE
Q psy15852        185 GKIFVGGLSPEM------KDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDK-EVD  256 (661)
Q Consensus       185 ~~lfV~nLp~~~------te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~-~i~  256 (661)
                      ++|||+|||..+      ++++|+++|++||+|.+|.++  +.+|+++|||||+|.+.++|.+|++.+ +..+.|+ +|.
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 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      789999999999999999988  457899999999999999999999986 6889998 876


Q ss_pred             E
Q psy15852        257 V  257 (661)
Q Consensus       257 V  257 (661)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=99.46  E-value=1.8e-13  Score=118.69  Aligned_cols=80  Identities=19%  Similarity=0.423  Sum_probs=72.7

Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                      .+..++|||+|||..+++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|++.+ +..+.|+.|.|.+
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            344689999999999999999999999999999999875      899999999999999999875 7899999999999


Q ss_pred             ccCCCCC
Q psy15852        260 ATPKPEP  266 (661)
Q Consensus       260 a~~k~~~  266 (661)
                      +.++...
T Consensus        96 a~~~~~~  102 (109)
T 1x4g_A           96 GKESPDM  102 (109)
T ss_dssp             CCCCCSS
T ss_pred             cCCCCCC
Confidence            9887654

>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=99.46  E-value=7e-14  Score=120.23  Aligned_cols=79  Identities=25%  Similarity=0.363  Sum_probs=70.7

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCC-CCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNT-GRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~t-g~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+++|.++++++++++|+++|++|| |.+|+|++++.+ ++++|||||+|.+.++|++|    + .+++..|.|+.|.|.
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A----~-~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           16 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA----L-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHH----H-GGGTCEETTEECEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHH----H-hcCCCEeCCcEEEEE
Confidence            4455555555999999999999999 999999999988 99999999999999999998    7 999999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        90 ~a~~~~   95 (104)
T 1wi8_A           90 VADQAQ   95 (104)
T ss_dssp             ECCCCC
T ss_pred             EccCCC
Confidence            987654

>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=99.46  E-value=4.3e-14  Score=122.00  Aligned_cols=81  Identities=28%  Similarity=0.320  Sum_probs=72.0

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeee---cceeeh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVI---NNKKIE  176 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i---~g~~i~  176 (661)
                      .++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..+   .+++|.
T Consensus        14 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A----~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           14 IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA----QSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHH----HHHHTTTCCCTTCSSCCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHH----HHHhcCCcccCCCCceEE
Confidence            3444545555999999999999999999999999999999999999999999999999    889999887   899999


Q ss_pred             hhhhhccC
Q psy15852        177 AKKAKAKS  184 (661)
Q Consensus       177 v~~~~~~~  184 (661)
                      |.++.++.
T Consensus        90 v~~a~~~~   97 (106)
T 2dgp_A           90 VKPADSES   97 (106)
T ss_dssp             EEECCCCS
T ss_pred             EEECCccc
Confidence            99987654

>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=99.46  E-value=6.6e-14  Score=116.31  Aligned_cols=80  Identities=23%  Similarity=0.351  Sum_probs=70.9

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCC-cccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGR-SRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~-srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .++++.++++++++++|+++|++||+|.+|+|+.++.++. ++|||||+|.+.++|++|    +..+++..+.|+.|.|.
T Consensus         5 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~v~   80 (88)
T 4a8x_A            5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA----LKHMDGGQIDGQEITAT   80 (88)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHH----HHHcCCCeECCeEEEEE
Confidence            3455555555999999999999999999999999887766 999999999999999999    88899999999999999


Q ss_pred             hhhcc
Q psy15852        179 KAKAK  183 (661)
Q Consensus       179 ~~~~~  183 (661)
                      ++.++
T Consensus        81 ~a~~~   85 (88)
T 4a8x_A           81 AVLAP   85 (88)
T ss_dssp             EECCC
T ss_pred             ECCCC
Confidence            88654

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

Probab=99.46  E-value=9.5e-14  Score=119.16  Aligned_cols=81  Identities=25%  Similarity=0.361  Sum_probs=72.7

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ...++++.++++++++++|+++|++||+|.+|+|+.+  +++++|||||+|.+.++|++|    +..+++..+.|+.|.|
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l~V   87 (103)
T 2d9p_A           14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKA----VTEMNGRIVATKPLYV   87 (103)
T ss_dssp             SCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHH----HHHHTTCBSSSSBCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHH----HHHhCCCEeCCcEEEE
Confidence            3455666666669999999999999999999999998  799999999999999999999    8889999999999999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .++.++.
T Consensus        88 ~~a~~~~   94 (103)
T 2d9p_A           88 ALAQRKE   94 (103)
T ss_dssp             EECSSCC
T ss_pred             EEecccc
Confidence            9987654

>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=99.46  E-value=6.1e-14  Score=120.55  Aligned_cols=82  Identities=20%  Similarity=0.321  Sum_probs=74.3

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+++++.++++++++++|+++|++||+|.+|+|++++.+|+++|||||+|.+.++|++|    +..+++..+.|+.|.|.
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~v~   83 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA----MRNLNGREFSGRALRVD   83 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHH----HHHSSSBSCSSSCBEEE
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHH----HHHhCCCeeCCcEEEEE
Confidence            35666666666999999999999999999999999988999999999999999999999    88899999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        84 ~a~~~~   89 (104)
T 1p1t_A           84 NAASEK   89 (104)
T ss_dssp             ETTCTT
T ss_pred             eCCCcc
Confidence            887653

>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=99.46  E-value=1.2e-13  Score=119.42  Aligned_cols=79  Identities=16%  Similarity=0.262  Sum_probs=70.2

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ...++++.++++.+++++|+++|++||+|.+|+|+.++ +|+++|||||+|.+.++|++|    +..+++..+.|+.|.|
T Consensus        28 ~~~~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           28 TGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKA----MKQYNGVPLDGRPMNI  102 (107)
T ss_dssp             CSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHH----HHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHH----HHHhCCCEeCCcEEEE
Confidence            34455555555599999999999999999999999998 799999999999999999999    8889999999999999


Q ss_pred             hhhh
Q psy15852        178 KKAK  181 (661)
Q Consensus       178 ~~~~  181 (661)
                      .++.
T Consensus       103 ~~a~  106 (107)
T 3ulh_A          103 QLVT  106 (107)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            8764

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

Probab=99.46  E-value=2.2e-13  Score=114.23  Aligned_cols=77  Identities=23%  Similarity=0.549  Sum_probs=69.5

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+++++++|+++|++||.|..|.++        ++||||+|.+.++|.+|++.+ +..+.|+.|.|.++
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            345799999999999999999999999999999996        449999999999999999875 68899999999999


Q ss_pred             cCCCCC
Q psy15852        261 TPKPEP  266 (661)
Q Consensus       261 ~~k~~~  266 (661)
                      .++...
T Consensus        80 ~~~~~~   85 (92)
T 2dgt_A           80 TSRLRT   85 (92)
T ss_dssp             SCCCSC
T ss_pred             cCCCCC
Confidence            887643

>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=99.46  E-value=1.1e-13  Score=117.82  Aligned_cols=58  Identities=10%  Similarity=0.046  Sum_probs=54.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhC
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED  655 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~  655 (661)
                      ..++|||+|||+++|+++|+++|++||.|.+|.|+++      ||||||+|.+.++|.+|++.+
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l   71 (101)
T 2cq1_A           14 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYY   71 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHh
Confidence            4678999999999999999999999999999999864      799999999999999999864

>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=99.46  E-value=2.8e-14  Score=125.10  Aligned_cols=84  Identities=17%  Similarity=0.301  Sum_probs=71.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||.++++++|+++|++||.|..+.+..+..+++++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++.
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~  103 (115)
T 2cpx_A           24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK  103 (115)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEcc
Confidence            4589999999999999999999999999843322222226889999999999999999999986 688999999999999


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++...
T Consensus       104 ~~~~~  108 (115)
T 2cpx_A          104 NKKQR  108 (115)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            87653

>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=99.46  E-value=1.7e-13  Score=116.14  Aligned_cols=76  Identities=21%  Similarity=0.409  Sum_probs=69.8

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccC--CeEEEEEe
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIN--DKEVDVKK  259 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~--g~~i~V~~  259 (661)
                      ..++|||+|||.++++++|+++|++||.|.+|.++.+      +|||||+|.+.++|++|++.+ +..+.  |+.|.|.+
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~   89 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEE
Confidence            4589999999999999999999999999999999753      789999999999999999975 68899  99999999


Q ss_pred             ccCCC
Q psy15852        260 ATPKP  264 (661)
Q Consensus       260 a~~k~  264 (661)
                      +.++.
T Consensus        90 a~~~~   94 (97)
T 1why_A           90 AKSGP   94 (97)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98865

>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=99.46  E-value=8.7e-14  Score=121.58  Aligned_cols=60  Identities=13%  Similarity=0.100  Sum_probs=55.2

Q ss_pred             cCCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        591 EAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       591 ~~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      ...++|||+|||+++||+||+++|++||.|.+|+|+++      ||||||+|.+.++|.+|++.++
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~   88 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYT   88 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhc
Confidence            34678999999999999999999999999999999975      7999999999999999998643

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.46  E-value=1.2e-14  Score=124.23  Aligned_cols=83  Identities=17%  Similarity=0.280  Sum_probs=74.7

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      ..++|||+|||+++++++|+++|++||.|.. .++.+..++.++|||||+|.+.++|.+|++.++..+.|+.|.|.++.+
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~   94 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKG   94 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECCSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEcCC
Confidence            3579999999999999999999999999888 677777789999999999999999999999447899999999999988


Q ss_pred             CCCC
Q psy15852        263 KPEP  266 (661)
Q Consensus       263 k~~~  266 (661)
                      +...
T Consensus        95 ~~~~   98 (101)
T 1fj7_A           95 RDGT   98 (101)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            6643

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

Probab=99.45  E-value=8.5e-14  Score=121.64  Aligned_cols=82  Identities=17%  Similarity=0.249  Sum_probs=72.7

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCee--------EEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeee
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIE--------NVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVI  170 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~--------~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i  170 (661)
                      ..+++|.++++++++++|+++|++||.|.        .|+|+.++.+++++|||||+|.+.++|++|    +..+++..|
T Consensus        15 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A----i~~l~g~~~   90 (113)
T 2cpe_A           15 NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAA----VEWFDGKDF   90 (113)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHH----HHHHTTCEE
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHH----HHHcCCCcc
Confidence            34455555555999999999999999999        699999988999999999999999999999    888999999


Q ss_pred             cceeehhhhhhccC
Q psy15852        171 NNKKIEAKKAKAKS  184 (661)
Q Consensus       171 ~g~~i~v~~~~~~~  184 (661)
                      .|+.|.|.++.++.
T Consensus        91 ~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           91 QGSKLKVSLARKKP  104 (113)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCCEEEEEECCCCC
Confidence            99999999987654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.45  E-value=1.1e-13  Score=119.78  Aligned_cols=78  Identities=12%  Similarity=0.153  Sum_probs=69.2

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCC-CeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFG-NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G-~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ..++|||+|||+++++++|+++|++|| +|..+.+..+    .++|||||+|.+.++|++|++.+ +..++|+.|.|.++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            457999999999999999999999999 9999998643    47999999999999999999886 67899999999998


Q ss_pred             cCCC
Q psy15852        261 TPKP  264 (661)
Q Consensus       261 ~~k~  264 (661)
                      ...+
T Consensus       103 ~~~p  106 (111)
T 2jvr_A          103 DNPP  106 (111)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            7543

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

Probab=99.45  E-value=1.5e-13  Score=122.09  Aligned_cols=81  Identities=11%  Similarity=0.242  Sum_probs=72.3

Q ss_pred             ccCCeeEecCCCccCCHHHHH----HHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIK----AHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVD  256 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~----~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~  256 (661)
                      +..++|||+|||+.+++++|+    ++|++||.|.+|.+..   +++++|||||+|.+.++|.+|++.+ +..+.|++|.
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            345799999999999999876    6999999999998864   4788999999999999999999887 6899999999


Q ss_pred             EEeccCCCC
Q psy15852        257 VKKATPKPE  265 (661)
Q Consensus       257 V~~a~~k~~  265 (661)
                      |.|+..+..
T Consensus       104 V~~a~~~~~  112 (127)
T 2a3j_A          104 ITFSETPQS  112 (127)
T ss_dssp             EEECCCCCH
T ss_pred             EEEccCcch
Confidence            999987654

>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=99.45  E-value=9e-14  Score=120.09  Aligned_cols=80  Identities=14%  Similarity=0.148  Sum_probs=70.8

Q ss_pred             hccCCeeEecCCCcc-CCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC---CCccCCeEEE
Q psy15852        181 KAKSGKIFVGGLSPE-MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP---KQKINDKEVD  256 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~---~~~~~g~~i~  256 (661)
                      .+..++|||+|||++ +++++|+++|++||.|.+|.|++      ++|||||+|.+.++|.+|++.+   +..+.|++|.
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            344689999999998 99999999999999999999964      4899999999999999999975   3579999999


Q ss_pred             EEeccCCCCC
Q psy15852        257 VKKATPKPEP  266 (661)
Q Consensus       257 V~~a~~k~~~  266 (661)
                      |.++..+...
T Consensus        96 V~~a~~~~~~  105 (112)
T 1x4f_A           96 VDLSEKYKKL  105 (112)
T ss_dssp             EEEECSCSSS
T ss_pred             EEECcccccc
Confidence            9999876643

>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=99.45  E-value=5.2e-14  Score=119.62  Aligned_cols=80  Identities=16%  Similarity=0.198  Sum_probs=71.1

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+++++.++.+|+++|||||+|.+.++|++|    +..+++..|.|+.|.|.+
T Consensus        16 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~A----i~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           16 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA----VIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             EEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHH----HHHTTTCEETTEECEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHH----HHHhCCCeeCCeEEEEEE
Confidence            3444444555999999999999999999999999888999999999999999999999    889999999999999998


Q ss_pred             hhcc
Q psy15852        180 AKAK  183 (661)
Q Consensus       180 ~~~~  183 (661)
                      +..+
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            7654

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

Probab=99.45  E-value=2.4e-13  Score=113.57  Aligned_cols=76  Identities=24%  Similarity=0.474  Sum_probs=69.2

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||+++++++|+++|++||.|..|.++        ++||||+|.+.++|++|++.+ +..++|+.|.|.++
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            345899999999999999999999999999999997        449999999999999999975 78999999999999


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .++..
T Consensus        79 ~~~~~   83 (90)
T 2dnp_A           79 TKGQK   83 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            88654

>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=99.45  E-value=2.7e-14  Score=123.57  Aligned_cols=82  Identities=16%  Similarity=0.157  Sum_probs=75.2

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCC---eEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGN---IIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~---i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~  258 (661)
                      ...++|||+|||+++++++|+++|++||.   |..|.|++++. |+++|||||+|.+.++|.+||+..+..++|+.|.|.
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~   87 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVY   87 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEEE
Confidence            34578999999999999999999999998   89999999987 999999999999999999999955789999999999


Q ss_pred             eccCCC
Q psy15852        259 KATPKP  264 (661)
Q Consensus       259 ~a~~k~  264 (661)
                      ++.++.
T Consensus        88 ~a~~~~   93 (107)
T 2lmi_A           88 EINNED   93 (107)
T ss_dssp             ECCHHH
T ss_pred             ECCHHH
Confidence            987654

>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=99.45  E-value=9.8e-14  Score=119.88  Aligned_cols=59  Identities=17%  Similarity=0.075  Sum_probs=54.3

Q ss_pred             cCCCeEEEcCCCCC-CCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhC
Q psy15852        591 EAKNKMVSHPGIVD-KITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED  655 (661)
Q Consensus       591 ~~~~~l~v~nlp~~-~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~  655 (661)
                      ...++|||+|||++ +|++||+++|++||.|.+|+|++      +||||||+|.+.++|.+|++.+
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l   82 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHC   82 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHh
Confidence            34689999999998 99999999999999999999974      4799999999999999999964

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

Probab=99.45  E-value=1.1e-13  Score=125.71  Aligned_cols=81  Identities=25%  Similarity=0.394  Sum_probs=73.0

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      ++++|.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|.+|    +..+++..|.|+.|.|.+
T Consensus        43 ~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA----IAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             SEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHH----HHHTTTEECSSCEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHH----HHHhCCCEECCeEEEEEE
Confidence            4455555555999999999999999999999999999999999999999999999999    888999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus       119 a~~~~  123 (139)
T 1u6f_A          119 AASGH  123 (139)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            87654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.45  E-value=6.4e-14  Score=120.00  Aligned_cols=60  Identities=25%  Similarity=0.455  Sum_probs=58.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHH
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASV  653 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~  653 (661)
                      .++|||+|||+++++++|+++|++||.|.+|+|++++ +|+++|||||+|.+.++|.+|++
T Consensus         9 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~   68 (102)
T 2xs2_A            9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE   68 (102)
T ss_dssp             EEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh
Confidence            5789999999999999999999999999999999998 89999999999999999999999

>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=99.45  E-value=1e-13  Score=115.21  Aligned_cols=79  Identities=25%  Similarity=0.555  Sum_probs=68.4

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      ...++|||+|||.++++++|+++|++||.|.+|.++.+     ++|||||+|.+.++|++|+.. ...+.|+.|.|.++.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecC
Confidence            34689999999999999999999999999999999864     689999999999999865433 456799999999998


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++...
T Consensus        77 ~~~~~   81 (88)
T 1wf0_A           77 PKHNS   81 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87643

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

Probab=99.45  E-value=1.9e-13  Score=114.57  Aligned_cols=79  Identities=18%  Similarity=0.308  Sum_probs=69.8

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+.|+++|+| ++++++|+++|++||+|.+|+|+++  +++++|||||+|.+.++|++|    +..+++..+.|+.|.|.
T Consensus         8 ~~~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            8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERA----CRMMNGMKLSGREIDVR   81 (92)
T ss_dssp             CCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHH----HHHHTTCCBTTBCCCCE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHH----HHHhCCCEECCcEEEEE
Confidence            3445555555 9999999999999999999999984  689999999999999999999    88999999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.+..
T Consensus        82 ~a~~~~   87 (92)
T 2dgv_A           82 IDRNAS   87 (92)
T ss_dssp             ECSCCS
T ss_pred             EcCCCC
Confidence            887643

>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=99.45  E-value=5.6e-14  Score=118.65  Aligned_cols=78  Identities=17%  Similarity=0.216  Sum_probs=69.6

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+++++.++.+++++|||||+|.++++|++|    +..+++..|.|++|.|.+
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~A----i~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           16 TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA----VIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             EEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHH----HHHHTTCEETTEECEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHH----HHHhCCCeECCcEEEEEe
Confidence            3444444555999999999999999999999999988999999999999999999999    888999999999999987


Q ss_pred             hh
Q psy15852        180 AK  181 (661)
Q Consensus       180 ~~  181 (661)
                      +.
T Consensus        92 a~   93 (95)
T 2ek1_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            64

>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=99.45  E-value=1.3e-13  Score=120.69  Aligned_cols=81  Identities=16%  Similarity=0.306  Sum_probs=73.8

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCcc--------CC
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKI--------ND  252 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~--------~g  252 (661)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|.+|++.+ +..+        .+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            345899999999999999999999999999999999998 8999999999999999999999976 5666        68


Q ss_pred             eEEEEEeccCC
Q psy15852        253 KEVDVKKATPK  263 (661)
Q Consensus       253 ~~i~V~~a~~k  263 (661)
                      ++|.|.++.++
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            88999999864

>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=99.44  E-value=6.2e-14  Score=119.64  Aligned_cols=79  Identities=25%  Similarity=0.393  Sum_probs=69.6

Q ss_pred             CCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCC-CCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852         99 KNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDP-NTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus        99 ~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~-~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ..+.|+++|++ ++++++|+++|++|| |.+|+|++++ .+|+++|||||+|.+.++|.+|    + .+++..+.|+.|.
T Consensus        18 ~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A----i-~l~g~~~~g~~l~   91 (100)
T 2j76_E           18 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA----L-SLNEESLGNRRIR   91 (100)
T ss_dssp             --CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHH----H-HTTTCCBTTBCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHH----H-hcCCCEECCeEEE
Confidence            34555555555 999999999999999 9999999998 5899999999999999999998    7 8999999999999


Q ss_pred             hhhhhcc
Q psy15852        177 AKKAKAK  183 (661)
Q Consensus       177 v~~~~~~  183 (661)
                      |.++.++
T Consensus        92 V~~a~~~   98 (100)
T 2j76_E           92 VDVADQA   98 (100)
T ss_dssp             CEECCCS
T ss_pred             EEeccCC
Confidence            9988765

>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=99.44  E-value=1.8e-13  Score=126.89  Aligned_cols=81  Identities=17%  Similarity=0.236  Sum_probs=72.7

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ...+|+|.++++++++++|+++|++||+|.+|+|+.++.+++++|||||+|.+.++|++|    +..+++..|.|+.|.|
T Consensus        38 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A----i~~l~g~~~~g~~l~V  113 (156)
T 1h2v_Z           38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA----MRYINGTRLDDRIIRT  113 (156)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH----HHHTTTSEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHH----HHHhCCCEECCeEEEE
Confidence            334555555555999999999999999999999999999999999999999999999999    8889999999999999


Q ss_pred             hhhhc
Q psy15852        178 KKAKA  182 (661)
Q Consensus       178 ~~~~~  182 (661)
                      .++.+
T Consensus       114 ~~a~~  118 (156)
T 1h2v_Z          114 DWDAG  118 (156)
T ss_dssp             EEESC
T ss_pred             EECCC
Confidence            98875

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

Probab=99.44  E-value=3.5e-14  Score=127.61  Aligned_cols=82  Identities=20%  Similarity=0.274  Sum_probs=72.5

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeE--EEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCe----eecce
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIEN--VTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH----VINNK  173 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~--v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~----~i~g~  173 (661)
                      .+++|.+|++++++++|+++|++||.|..  |+|++|+.||++||||||+|.+. +|.+|    +..+++.    .+.|+
T Consensus        24 ~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~A----i~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           24 DTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQL----LQILQALHPPLTIDGK   98 (131)
T ss_dssp             CEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHH----HHHHTTCCCSCCGGGC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHH----HHHhcCCCCCccCCCE
Confidence            44444444459999999999999999977  99999999999999999999999 99999    9999999    99999


Q ss_pred             eehhhhhhccCCe
Q psy15852        174 KIEAKKAKAKSGK  186 (661)
Q Consensus       174 ~i~v~~~~~~~~~  186 (661)
                      .|.|.++.+..+.
T Consensus        99 ~l~V~~a~~~~~~  111 (131)
T 2m2b_A           99 TINVEFAKGSKRD  111 (131)
T ss_dssp             CCCCEECCCSCCC
T ss_pred             EEEEEECCCCCCC
Confidence            9999999876543

>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=99.44  E-value=1.8e-14  Score=128.14  Aligned_cols=82  Identities=16%  Similarity=0.197  Sum_probs=74.2

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      ..++|||+|||+++++++|+++|++||.|..+.++.+..+++++|||||+|.+.++|.+||+.++..|+|+.|.|.++.+
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a~~  103 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITK  103 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEECH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECCH
Confidence            34799999999999999999999999999886666667789999999999999999999999557899999999999876


Q ss_pred             CC
Q psy15852        263 KP  264 (661)
Q Consensus       263 k~  264 (661)
                      +.
T Consensus       104 ~~  105 (124)
T 1wel_A          104 KG  105 (124)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>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=99.44  E-value=1.6e-13  Score=119.25  Aligned_cols=73  Identities=15%  Similarity=0.455  Sum_probs=67.4

Q ss_pred             CCeeEecCCCcc-CCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        184 SGKIFVGGLSPE-MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       184 ~~~lfV~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      .++|||+|||+. +++++|+++|++||.|..|.+        ++|||||+|.+.++|++|++.+ +..++|+.|.|.++.
T Consensus        27 ~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   98 (110)
T 1wf1_A           27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAG   98 (110)
T ss_dssp             SSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            379999999999 999999999999999999998        4899999999999999999775 789999999999998


Q ss_pred             CCC
Q psy15852        262 PKP  264 (661)
Q Consensus       262 ~k~  264 (661)
                      ++.
T Consensus        99 ~~~  101 (110)
T 1wf1_A           99 EPK  101 (110)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>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=99.44  E-value=2.9e-14  Score=119.16  Aligned_cols=79  Identities=24%  Similarity=0.419  Sum_probs=69.5

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      ++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.+ |.+|    +..+++..+.|++|.|.++
T Consensus         3 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a----~~~l~g~~~~g~~l~V~~a   77 (90)
T 2ki2_A            3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEA----IAKLDNTDFMGRTIRVTEA   77 (90)
T ss_dssp             EEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHH----HHTSCSSCCSSSSCSEEEC
T ss_pred             EEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHH----HHHhCCCEECCeEEEEEEc
Confidence            4555555669999999999999999999999999999999999999999999 9999    8999999999999999998


Q ss_pred             hccC
Q psy15852        181 KAKS  184 (661)
Q Consensus       181 ~~~~  184 (661)
                      .+..
T Consensus        78 ~~~~   81 (90)
T 2ki2_A           78 NPKK   81 (90)
T ss_dssp             ----
T ss_pred             CCCC
Confidence            7643

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.44  E-value=8.8e-14  Score=120.56  Aligned_cols=60  Identities=23%  Similarity=0.309  Sum_probs=55.1

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcC----HHH----HHHHHH
Q psy15852        594 NKMVSHPG----IVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKD----TES----LEKASV  653 (661)
Q Consensus       594 ~~l~v~nl----p~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~----~e~----A~~A~~  653 (661)
                      ++|||+||    |+.++|++|+++|++||+|.+|+++.|+.||+|+|||||+|.+    +++    |.+|+.
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~   74 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVR   74 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHH
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHH
Confidence            68999999    9999999999999999999999999999999999999999996    444    788877

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

Probab=99.44  E-value=2.7e-13  Score=118.55  Aligned_cols=80  Identities=18%  Similarity=0.215  Sum_probs=72.2

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ...+++|.++++++++++|+++|++||+|.+|+|+.++ +++++|||||+|.+.++|++|    +..+++..|.|+.|.|
T Consensus        14 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~v   88 (114)
T 2do0_A           14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQA----ISMFNGQLLFDRPMHV   88 (114)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHH----HHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHH----HHHhCCCEeCCCEEEE
Confidence            34566666666699999999999999999999999987 499999999999999999999    8889999999999999


Q ss_pred             hhhhc
Q psy15852        178 KKAKA  182 (661)
Q Consensus       178 ~~~~~  182 (661)
                      .++..
T Consensus        89 ~~a~~   93 (114)
T 2do0_A           89 KMDER   93 (114)
T ss_dssp             EECSC
T ss_pred             EEccc
Confidence            98764

>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=99.44  E-value=2.1e-13  Score=116.08  Aligned_cols=78  Identities=24%  Similarity=0.442  Sum_probs=70.9

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +..++|||+|||+.+++++|+++|++||+|..|.++++      +|||||+|.+.++|.+|++.+ +..+.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            34579999999999999999999999999999999753      899999999999999999875 68899999999999


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .++..
T Consensus        87 ~~~~~   91 (99)
T 2cpj_A           87 CHSAS   91 (99)
T ss_dssp             SCCSC
T ss_pred             CCCCC
Confidence            88654

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

Probab=99.44  E-value=1.3e-13  Score=121.05  Aligned_cols=80  Identities=26%  Similarity=0.513  Sum_probs=71.4

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .+++|.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +.. ++..|.|+.|.|.+
T Consensus        28 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A----i~~-~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA----MAA-RPHSIDGRVVEPKR  102 (116)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHH----HTS-CSEEETTEEEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHH----HHh-CCcEECCEEEEEEE
Confidence            4555555555999999999999999999999999999999999999999999999997    665 99999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus       103 a~~~~  107 (116)
T 1x4b_A          103 AVARE  107 (116)
T ss_dssp             CSSCC
T ss_pred             CCCCc
Confidence            87654

>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=99.44  E-value=2.3e-13  Score=116.79  Aligned_cols=80  Identities=14%  Similarity=0.169  Sum_probs=69.9

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|++++.  .++|||||+|.+.++|++|    +..+++..|.|+.|.|.
T Consensus        15 ~~~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           15 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAA----LAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHH----HHHHTTEEETTEEEEEE
T ss_pred             CCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHH----HHHhCCCCcCCCeEEEE
Confidence            34555555555999999999999999999999999854  4799999999999999999    88899999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        89 ~a~~~~   94 (103)
T 2cqi_A           89 WATTPS   94 (103)
T ss_dssp             ECCCTT
T ss_pred             ECCCCc
Confidence            987654

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

Probab=99.44  E-value=1e-13  Score=117.26  Aligned_cols=77  Identities=19%  Similarity=0.461  Sum_probs=69.2

Q ss_pred             ccCCeeEecCCCc-cCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        182 AKSGKIFVGGLSP-EMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       182 ~~~~~lfV~nLp~-~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                      +..++|||+|||+ .+++++|+++|++||.|..|.+.        +|||||+|.+.++|.+|++.+ +..+.|+.|.|.+
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            4568999999998 99999999999999999999983        789999999999999999975 6889999999999


Q ss_pred             ccCCCCC
Q psy15852        260 ATPKPEP  266 (661)
Q Consensus       260 a~~k~~~  266 (661)
                      +.++..+
T Consensus        80 a~~~~~~   86 (96)
T 2kvi_A           80 SSSNARP   86 (96)
T ss_dssp             EECCCC-
T ss_pred             cCcCCCC
Confidence            9876543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=3.2e-13  Score=113.77  Aligned_cols=79  Identities=16%  Similarity=0.324  Sum_probs=68.4

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      ..++|||+|||+++++++|+++|++||.|.+|  +.++.+++   ||||+|.+.++|.+|++..+..++|+.|.|.++.+
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~~   81 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQ   81 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECCc
Confidence            34799999999999999999999999999987  44555444   99999999999999999447899999999999877


Q ss_pred             CCCC
Q psy15852        263 KPEP  266 (661)
Q Consensus       263 k~~~  266 (661)
                      +...
T Consensus        82 ~~~~   85 (94)
T 2e5g_A           82 KEFQ   85 (94)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            6543

>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=99.44  E-value=1.3e-13  Score=119.97  Aligned_cols=82  Identities=20%  Similarity=0.289  Sum_probs=73.5

Q ss_pred             CCcEEEEcCCCcCCHHHHH---HHhhcCCCeeEEEEeeCCCCC---CcccEEEEEEeehhhHHHhhHHHHHHhCCeeecc
Q psy15852         99 KNKMVSHPGIVHKITEELK---EHFSKYGEIENVTLKSDPNTG---RSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN  172 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~---~~F~~~G~I~~v~l~~~~~tg---~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g  172 (661)
                      ..++++.++++++++++|+   ++|++||+|.+|+|++++.++   +++|||||+|.+.++|++|    +..+|+..|.|
T Consensus        15 ~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~A----i~~lng~~~~g   90 (111)
T 2cpi_A           15 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRA----IQCVNNVVVDG   90 (111)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHH----HHHHTTEEETT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHH----HHHhCCCEECC
Confidence            4567777777799999999   999999999999999987654   5669999999999999999    89999999999


Q ss_pred             eeehhhhhhccC
Q psy15852        173 KKIEAKKAKAKS  184 (661)
Q Consensus       173 ~~i~v~~~~~~~  184 (661)
                      ++|.|.++.++.
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            999999998765

>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=99.44  E-value=1.7e-13  Score=115.96  Aligned_cols=77  Identities=21%  Similarity=0.174  Sum_probs=68.2

Q ss_pred             cEEEEcCCCcCCHHHHH----HHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852        101 KMVSHPGIVHKITEELK----EHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~----~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ++++.++++++++++|+    ++|++||+|.+|+|+.++.+   ||||||+|.+.++|++|    +..+|+..+.|++|.
T Consensus        11 ~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~A----i~~l~g~~~~gr~l~   83 (96)
T 2dgx_A           11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGA----VNSLHRYKIGSKKIL   83 (96)
T ss_dssp             EEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHH----HHHHTTEEETTEEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHH----HHHhCCCEECCeEEE
Confidence            44444445599999999    99999999999999998764   89999999999999999    899999999999999


Q ss_pred             hhhhhccC
Q psy15852        177 AKKAKAKS  184 (661)
Q Consensus       177 v~~~~~~~  184 (661)
                      |.++.+..
T Consensus        84 V~~a~~~~   91 (96)
T 2dgx_A           84 VSLATGAS   91 (96)
T ss_dssp             EEECCCSS
T ss_pred             EEEcCCCC
Confidence            99987654

>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=99.44  E-value=2.1e-13  Score=116.78  Aligned_cols=58  Identities=16%  Similarity=0.174  Sum_probs=53.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhC
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED  655 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~  655 (661)
                      +.++|||+|||++++|++|+++|++||.|.+|.|+++      ||||||+|.+.++|.+|++.+
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l   71 (104)
T 1wex_A           14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFA   71 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHh
Confidence            4578999999999999999999999999999999863      789999999999999999864

>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=99.44  E-value=1.2e-13  Score=123.12  Aligned_cols=81  Identities=17%  Similarity=0.315  Sum_probs=72.4

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .+|+|.++++++++++|+++|++||.|.+|.|+.++.++.++|||||+|.+.++|++|    +..+++..|.|+.|.|.+
T Consensus        23 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           23 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA----MEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHH----HHHHTTCBSSSSBCEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHH----HHHhCCCeeCCeEEEEEE
Confidence            3444445555999999999999999999999999998999999999999999999999    889999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        99 a~~~~  103 (126)
T 3ex7_B           99 CFVRG  103 (126)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            87653

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

Probab=99.44  E-value=5.3e-13  Score=113.54  Aligned_cols=76  Identities=16%  Similarity=0.369  Sum_probs=68.8

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcC--CCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQF--GNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~--G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~  258 (661)
                      ...++|||+|||+.+++++|+++|++|  |.|..|.++        +|||||+|.+.++|.+|++.+ +..+.|+.|.|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT   84 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            345899999999999999999999999  999999874        679999999999999999965 688999999999


Q ss_pred             eccCCCC
Q psy15852        259 KATPKPE  265 (661)
Q Consensus       259 ~a~~k~~  265 (661)
                      ++.++..
T Consensus        85 ~a~~~~~   91 (99)
T 2cpd_A           85 LAKPVDK   91 (99)
T ss_dssp             CCCCCCC
T ss_pred             ECCCCCC
Confidence            9987654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.43  E-value=1.7e-13  Score=118.73  Aligned_cols=80  Identities=24%  Similarity=0.295  Sum_probs=65.0

Q ss_pred             cEEEEcC----CCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEee----hhhHHHhhHHHHH--HhCCeee
Q psy15852        101 KMVSHPG----IVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKD----TESLEKASVEDVI--AEGNHVI  170 (661)
Q Consensus       101 ~~~~~~~----~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~----~e~A~~A~~~~~~--~~~~~~i  170 (661)
                      +++|.++    ++.+++++|+++|++||+|.+|.++.|+.||+++|||||+|.+    +++|.+|...++.  .+++..|
T Consensus         4 kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I   83 (136)
T 2j8a_A            4 EIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFI   83 (136)
T ss_dssp             EEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEE
T ss_pred             EEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCee
Confidence            4566666    6799999999999999999999999999999999999999997    5553322222277  6899999


Q ss_pred             cceeehhhhh
Q psy15852        171 NNKKIEAKKA  180 (661)
Q Consensus       171 ~g~~i~v~~~  180 (661)
                      .|++|.|..-
T Consensus        84 ~Gr~irV~ln   93 (136)
T 2j8a_A           84 MGFKFEVILN   93 (136)
T ss_dssp             TTEEEEEEEC
T ss_pred             cCcEEEEEEC
Confidence            9999998643

>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=99.43  E-value=3.3e-13  Score=115.70  Aligned_cols=80  Identities=21%  Similarity=0.396  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|++++.  .++|||||+|.+.++|++|    +..+++..|.|+.|.|.
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~v~   88 (103)
T 2cq3_A           15 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRA----REKLHGTVVEGRKIEVN   88 (103)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHH----HHHhCCCEECCEEEEEE
Confidence            34455555555999999999999999999999999864  4999999999999999999    88999999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        89 ~a~~~~   94 (103)
T 2cq3_A           89 NATARV   94 (103)
T ss_dssp             ECCSSC
T ss_pred             EcccCC
Confidence            987654

>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=99.43  E-value=2e-13  Score=119.63  Aligned_cols=81  Identities=10%  Similarity=0.206  Sum_probs=73.4

Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                      .+..++|||+|||+.+++++|+++|++||.|.+|.++.+   +.++|||||+|.+.++|.+|++.+ +..++|+.|.|.+
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            345689999999999999999999999999999999876   455999999999999999999965 7899999999999


Q ss_pred             ccCCC
Q psy15852        260 ATPKP  264 (661)
Q Consensus       260 a~~k~  264 (661)
                      +.++.
T Consensus        82 a~~~~   86 (115)
T 3lqv_A           82 YNANR   86 (115)
T ss_dssp             CCHHH
T ss_pred             ecCCh
Confidence            98754

>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=99.43  E-value=1.7e-13  Score=115.15  Aligned_cols=78  Identities=14%  Similarity=0.358  Sum_probs=68.4

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCC-eEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-C-CccCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGN-IIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-K-QKINDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~-i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~-~~~~g~~i~V~  258 (661)
                      ...++|||+|||+++++++|+++|++||. |..+.+.       ++|||||+|.+.++|.+|++.+ + ..++|+.|.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            34579999999999999999999999999 6666652       4899999999999999999876 6 78999999999


Q ss_pred             eccCCCCC
Q psy15852        259 KATPKPEP  266 (661)
Q Consensus       259 ~a~~k~~~  266 (661)
                      ++.++..+
T Consensus        79 ~a~~~~~~   86 (93)
T 2cqh_A           79 YSVSKKLR   86 (93)
T ss_dssp             ECCCCCCC
T ss_pred             EccCcccc
Confidence            99887543

>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=99.43  E-value=1.7e-13  Score=116.12  Aligned_cols=82  Identities=21%  Similarity=0.410  Sum_probs=73.6

Q ss_pred             hccCCeeEecCCCccCCHHHHH----HHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEE
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIK----AHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEV  255 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~----~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i  255 (661)
                      .+..++|||+|||.++++++|+    ++|++||.|..|.++.   ++.++|||||+|.+.++|.+|++.+ +..+.|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            3456899999999999999999    9999999999999874   4778999999999999999999975 789999999


Q ss_pred             EEEeccCCCC
Q psy15852        256 DVKKATPKPE  265 (661)
Q Consensus       256 ~V~~a~~k~~  265 (661)
                      .|.++.++..
T Consensus        82 ~v~~a~~~~~   91 (97)
T 1nu4_A           82 RIQYAKTDSD   91 (97)
T ss_dssp             EEEECSSCCT
T ss_pred             EEEEccCCCc
Confidence            9999988654

>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=99.43  E-value=9.3e-14  Score=118.23  Aligned_cols=59  Identities=17%  Similarity=0.093  Sum_probs=54.4

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        592 AKNKMVSHPGIV-DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       592 ~~~~l~v~nlp~-~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      +.++|||+|||+ ++||+||+++|++||.|.+|+|+++      +|||||+|.+.++|.+|++.++
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~   73 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYT   73 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHc
Confidence            467899999999 9999999999999999999999975      4799999999999999999654

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

Probab=99.42  E-value=2.1e-13  Score=121.25  Aligned_cols=79  Identities=24%  Similarity=0.433  Sum_probs=71.5

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    + .+++..|.|+.|.|.+
T Consensus        37 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A----~-~l~g~~~~g~~l~V~~  111 (124)
T 2jwn_A           37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA----V-AMDETVFRGRTIKVLP  111 (124)
T ss_dssp             TEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHH----H-TTTTCEETTEECEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHH----H-hcCCCeECCeEEEEEE
Confidence            4555555556999999999999999999999999988999999999999999999998    7 8999999999999998


Q ss_pred             hhcc
Q psy15852        180 AKAK  183 (661)
Q Consensus       180 ~~~~  183 (661)
                      +.+.
T Consensus       112 a~~~  115 (124)
T 2jwn_A          112 KRTN  115 (124)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            8754

>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=99.42  E-value=2.2e-13  Score=113.43  Aligned_cols=57  Identities=28%  Similarity=0.446  Sum_probs=52.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHH
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASV  653 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~  653 (661)
                      ..++|||+|||+++||++|+++|++||.|.+|+|+++     +||||||+|.+.++|.++..
T Consensus        10 ~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~   66 (89)
T 3d2w_A           10 HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG   66 (89)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcC
Confidence            4689999999999999999999999999999999974     79999999999999996543

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

Probab=99.42  E-value=1.9e-13  Score=116.86  Aligned_cols=76  Identities=12%  Similarity=0.299  Sum_probs=69.2

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +..++|||+|||.++++++|+++|++||.|.+|.+.      +++|||||+|.+.++|.+|+..+ +..++|+.|.|.|+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            345899999999999999999999999999999996      35899999999999999999875 78999999999998


Q ss_pred             cCC
Q psy15852        261 TPK  263 (661)
Q Consensus       261 ~~k  263 (661)
                      .++
T Consensus        99 ~~~  101 (101)
T 2la4_A           99 KER  101 (101)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=3.6e-13  Score=112.65  Aligned_cols=77  Identities=13%  Similarity=0.265  Sum_probs=68.8

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++| .|.+|+|+++ .+|+++|||||+|.+.++|++|    +. +++..|.|+.|.|.+
T Consensus        11 ~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A----~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A           11 HTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQA----LK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHH----HH-SCSEEETTEEEEEEE
T ss_pred             cEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHH----HH-hCCceeCCcEEEEEE
Confidence            445555555599999999999999 9999999998 6799999999999999999998    77 999999999999998


Q ss_pred             hhcc
Q psy15852        180 AKAK  183 (661)
Q Consensus       180 ~~~~  183 (661)
                      +.++
T Consensus        84 a~~~   87 (91)
T 2dgw_A           84 EKSG   87 (91)
T ss_dssp             ESSC
T ss_pred             CCcC
Confidence            8765

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

Probab=99.41  E-value=3.2e-13  Score=120.10  Aligned_cols=79  Identities=16%  Similarity=0.269  Sum_probs=70.7

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+|+|+.++ +|+++|||||+|.+.++|++|    +..+++..+.|+.|.|.+
T Consensus        36 ~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A----i~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKA----MKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             EEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHH----HHHHTTEESSSCEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHH----HHHcCCCEECCcEEEEEE
Confidence            344444445599999999999999999999999998 899999999999999999999    888999999999999998


Q ss_pred             hhcc
Q psy15852        180 AKAK  183 (661)
Q Consensus       180 ~~~~  183 (661)
                      +.+.
T Consensus       111 a~~~  114 (124)
T 2kt5_A          111 VASQ  114 (124)
T ss_dssp             ECCT
T ss_pred             eCCC
Confidence            8754

>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=99.41  E-value=6.9e-13  Score=127.27  Aligned_cols=79  Identities=14%  Similarity=0.297  Sum_probs=74.0

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK  263 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k  263 (661)
                      .++|||+|||+++++++|+++|++||+|..|.++++.. +.++|||||+|.+.++|.+|++.++..++|+.|.|.++..-
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~-~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDY  187 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTT-CCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCC-CCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHHH
Confidence            37899999999999999999999999999999998764 88999999999999999999998888999999999998764

>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=99.41  E-value=5.6e-13  Score=109.91  Aligned_cols=74  Identities=24%  Similarity=0.458  Sum_probs=67.7

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC--CCccCCeEEEEEe
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP--KQKINDKEVDVKK  259 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~--~~~~~g~~i~V~~  259 (661)
                      +..++|||+|||..+++++|+++|++||.|..|.+++      ++|||||+|.+.++|.+|++.+  +..++|++|.|.|
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~------~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ------RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC------CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            4458999999999999999999999999999999986      3899999999999999999975  5789999999999


Q ss_pred             cc
Q psy15852        260 AT  261 (661)
Q Consensus       260 a~  261 (661)
                      ++
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.41  E-value=1.9e-13  Score=115.65  Aligned_cols=78  Identities=18%  Similarity=0.262  Sum_probs=69.7

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||..+++++|+++|++||.|..+     ..++.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++.
T Consensus        15 ~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   89 (96)
T 1fjc_A           15 AARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcC
Confidence            35799999999999999999999999988766     335889999999999999999999976 578999999999998


Q ss_pred             CCCC
Q psy15852        262 PKPE  265 (661)
Q Consensus       262 ~k~~  265 (661)
                      ++..
T Consensus        90 ~~~~   93 (96)
T 1fjc_A           90 EKGG   93 (96)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            7653

>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=99.41  E-value=7.4e-13  Score=112.18  Aligned_cols=75  Identities=19%  Similarity=0.435  Sum_probs=68.6

Q ss_pred             hccCCeeEecCCCc-cCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEE
Q psy15852        181 KAKSGKIFVGGLSP-EMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVK  258 (661)
Q Consensus       181 ~~~~~~lfV~nLp~-~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~  258 (661)
                      .+..++|||+|||. ++++++|+++|++||.|..|.+.        +|||||+|.+.++|.+|++.+ +..+.|+.|.|.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44568999999998 99999999999999999999983        799999999999999999976 678999999999


Q ss_pred             eccCC
Q psy15852        259 KATPK  263 (661)
Q Consensus       259 ~a~~k  263 (661)
                      ++.++
T Consensus        91 ~a~~~   95 (97)
T 2xnq_A           91 VSSSN   95 (97)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            98765

>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=99.40  E-value=3.4e-13  Score=118.19  Aligned_cols=75  Identities=19%  Similarity=0.359  Sum_probs=64.5

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeE-----EE
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKE-----VD  256 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~-----i~  256 (661)
                      ..++|||+|||+++++++|+++|++||+|..|.|+.+       |||||+|.+.++|++||+.+ +..|+|+.     |.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            3579999999999999999999999999999999764       99999999999999999976 68899988     77


Q ss_pred             EEeccCCC
Q psy15852        257 VKKATPKP  264 (661)
Q Consensus       257 V~~a~~k~  264 (661)
                      |..+.++.
T Consensus        88 v~~~~~~~   95 (115)
T 3beg_B           88 VKVDGPRS   95 (115)
T ss_dssp             EEECC---
T ss_pred             eccCCCCC
Confidence            77766543

>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=99.40  E-value=5.4e-13  Score=115.71  Aligned_cols=79  Identities=20%  Similarity=0.323  Sum_probs=68.6

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..+++|.++++++++++|+++|++||+|.+|+|+.+   ++++|||||+|.+.++|++|    +..+++..|.|+.|.|.
T Consensus        22 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           22 DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDA----VYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHH----HHHcCCCEECCeEEEEE
Confidence            344555555559999999999999999999999764   56899999999999999999    88999999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        95 ~a~~~~  100 (109)
T 1x4a_A           95 FPRSGR  100 (109)
T ss_dssp             CCCCCC
T ss_pred             EcccCC
Confidence            987653

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.40  E-value=2.9e-13  Score=114.73  Aligned_cols=78  Identities=10%  Similarity=0.299  Sum_probs=69.3

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +..++|||+|||+.+++++|+++|++||.|. +.++.    +.++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            3458999999999999999999999999996 66654    467999999999999999999875 78999999999999


Q ss_pred             cCCC
Q psy15852        261 TPKP  264 (661)
Q Consensus       261 ~~k~  264 (661)
                      .++.
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

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

Probab=99.40  E-value=3.7e-13  Score=115.91  Aligned_cols=78  Identities=15%  Similarity=0.265  Sum_probs=67.3

Q ss_pred             CcEEEEcCCCcC------CHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecce
Q psy15852        100 NKMVSHPGIVHK------ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK  173 (661)
Q Consensus       100 ~~~~~~~~~~~~------te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~  173 (661)
                      .++++.++++.+      ++++|+++|++||+|.+|+|+  +.+|+++|||||+|.+.++|.+|    +..+|+..+.|+
T Consensus        16 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~A----i~~l~g~~~~g~   89 (105)
T 2nlw_A           16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDA----VKNADGYKLDKQ   89 (105)
T ss_dssp             SEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHH----HHHCSSEECSTT
T ss_pred             CEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHH----HHHhCCcccCCC
Confidence            344444444577      789999999999999999998  35799999999999999999999    899999999998


Q ss_pred             -eehhhhhhcc
Q psy15852        174 -KIEAKKAKAK  183 (661)
Q Consensus       174 -~i~v~~~~~~  183 (661)
                       +|.|.++...
T Consensus        90 ~~l~V~~a~~~  100 (105)
T 2nlw_A           90 HTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECSCCC
T ss_pred             ceEEEEEcchH
Confidence             9999888653

>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=99.40  E-value=5.1e-13  Score=125.07  Aligned_cols=80  Identities=25%  Similarity=0.346  Sum_probs=72.2

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      +|+|.+|++.+++++|+++|++||+|.+|.|+.++.+|+++|||||+|.+.++|++|    +..+++..|.|+.|.|.++
T Consensus        74 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A----i~~l~g~~~~g~~l~V~~a  149 (165)
T 1rk8_A           74 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA----KEALNGAEIMGQTIQVDWC  149 (165)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHH----HHHHTTCEETTEECEEEES
T ss_pred             EEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHH----HHHhCCCEECCEEEEEEEe
Confidence            445555555999999999999999999999999999999999999999999999999    8899999999999999998


Q ss_pred             hccC
Q psy15852        181 KAKS  184 (661)
Q Consensus       181 ~~~~  184 (661)
                      .++.
T Consensus       150 ~~~~  153 (165)
T 1rk8_A          150 FVKG  153 (165)
T ss_dssp             EECC
T ss_pred             cCCC
Confidence            7653

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

Probab=99.40  E-value=5.7e-13  Score=115.28  Aligned_cols=76  Identities=16%  Similarity=0.396  Sum_probs=69.4

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||.++++++|+++|++||.|..|.++        +|||||+|.+.++|.+|++.+ +..++|+.|.|.++
T Consensus        29 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  100 (108)
T 2jvo_A           29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS  100 (108)
T ss_dssp             CSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            345899999999999999999999999999999996        799999999999999999975 78999999999999


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .++..
T Consensus       101 ~~~~~  105 (108)
T 2jvo_A          101 KLPAK  105 (108)
T ss_dssp             SCCC-
T ss_pred             cCCCC
Confidence            87653

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

Probab=99.40  E-value=5.6e-13  Score=116.61  Aligned_cols=79  Identities=29%  Similarity=0.529  Sum_probs=68.8

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCC---CCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSK---SQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~---g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~  258 (661)
                      ...++|||+|||+++++++|+++|++||+|. +.++.+..+   |+++|||||+|.+.++|++||+.+ ..++|+.|.+.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~-~~~~G~~~~~~   83 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC-LEEDGKLYLCV   83 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS-EEETTEEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh-hhcCCcEEEec
Confidence            3468999999999999999999999999999 888888877   799999999999999999999987 34677777776


Q ss_pred             eccC
Q psy15852        259 KATP  262 (661)
Q Consensus       259 ~a~~  262 (661)
                      .+.+
T Consensus        84 ~~~~   87 (114)
T 2dnl_A           84 SSPT   87 (114)
T ss_dssp             CCSS
T ss_pred             cCCC
Confidence            5443

>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=99.39  E-value=4.7e-13  Score=116.43  Aligned_cols=75  Identities=15%  Similarity=0.159  Sum_probs=68.9

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      .++|||+|||+.+++++|+++|++||.|..|.|+.      ++|||||+|.+.++|.+|++.+ +..+.|+.|.|.|+..
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            46899999999999999999999999999999864      4889999999999999999976 6889999999999987


Q ss_pred             CC
Q psy15852        263 KP  264 (661)
Q Consensus       263 k~  264 (661)
                      ..
T Consensus        84 ~~   85 (111)
T 1whx_A           84 GV   85 (111)
T ss_dssp             TT
T ss_pred             Cc
Confidence            54

>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=99.39  E-value=2.9e-13  Score=133.53  Aligned_cols=79  Identities=15%  Similarity=0.176  Sum_probs=71.1

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCC--CeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYG--EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G--~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      .+|||.+|++++|+++|+++|++||  .|.+|+|++++.++++||||||+|.+.++|++|    +..+|+..|.|+.|.|
T Consensus        69 ~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~A----i~~lng~~~~Gr~l~V  144 (229)
T 3q2s_C           69 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL----MDLLPKRELHGQNPVV  144 (229)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHH----HTTSTTSCBTTBCCEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHH----HHHcCCCeECCEEeEE
Confidence            3455555555999999999999999  999999999999999999999999999999999    8889999999999999


Q ss_pred             hhhhc
Q psy15852        178 KKAKA  182 (661)
Q Consensus       178 ~~~~~  182 (661)
                      .++.+
T Consensus       145 ~~a~~  149 (229)
T 3q2s_C          145 TPVNK  149 (229)
T ss_dssp             EECCH
T ss_pred             EECCC
Confidence            88764

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

Probab=99.39  E-value=5.6e-13  Score=126.03  Aligned_cols=81  Identities=19%  Similarity=0.391  Sum_probs=75.8

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||+.+++++|+++|++||.|..|.|+.+. ++.++|||||+|.+.++|.+|++.+ +..++|+.|.|.++.
T Consensus        87 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            35799999999999999999999999999999999988 8999999999999999999999976 689999999999998


Q ss_pred             CCC
Q psy15852        262 PKP  264 (661)
Q Consensus       262 ~k~  264 (661)
                      ...
T Consensus       166 ~~~  168 (177)
T 2f3j_A          166 SQI  168 (177)
T ss_dssp             SGG
T ss_pred             CCC
Confidence            754

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

Probab=99.39  E-value=4.5e-13  Score=116.17  Aligned_cols=78  Identities=22%  Similarity=0.407  Sum_probs=68.7

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+|+|++++  +.++|||||+|.+.++|++|    +..+++..+.|+.|.|.+
T Consensus        30 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~A----i~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRA----REKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             CEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHH----HHHHTTCEETTEECEEEE
T ss_pred             CEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHH----HHHcCCCEECCEEEEEEE
Confidence            444454455599999999999999999999999985  45999999999999999999    888999999999999998


Q ss_pred             hhcc
Q psy15852        180 AKAK  183 (661)
Q Consensus       180 ~~~~  183 (661)
                      +.++
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.38  E-value=2.2e-12  Score=109.29  Aligned_cols=75  Identities=24%  Similarity=0.448  Sum_probs=67.9

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+||  ++++++|+++|++||+|..|.|.      .++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++.
T Consensus        14 ~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~   85 (97)
T 1x5p_A           14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   85 (97)
T ss_dssp             CCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCS
T ss_pred             CCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECC
Confidence            4579999996  89999999999999999999984      46899999999999999999886 678999999999998


Q ss_pred             CCCC
Q psy15852        262 PKPE  265 (661)
Q Consensus       262 ~k~~  265 (661)
                      ++..
T Consensus        86 ~~~~   89 (97)
T 1x5p_A           86 KQPM   89 (97)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8654

>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=99.38  E-value=8.9e-13  Score=113.91  Aligned_cols=79  Identities=11%  Similarity=0.163  Sum_probs=69.1

Q ss_pred             ccCCeeEe--cCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCcc-----CCe
Q psy15852        182 AKSGKIFV--GGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKI-----NDK  253 (661)
Q Consensus       182 ~~~~~lfV--~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~-----~g~  253 (661)
                      .+.++|||  +||++.+++++|+++|++||.|.+|.++.      .+|||||+|.+.++|++|++.+ +..+     .|+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            44678999  67999999999999999999999998864      2799999999999999999987 5666     689


Q ss_pred             EEEEEeccCCCCC
Q psy15852        254 EVDVKKATPKPEP  266 (661)
Q Consensus       254 ~i~V~~a~~k~~~  266 (661)
                      +|.|.++...+..
T Consensus        97 ~l~v~~a~~~p~~  109 (114)
T 2cq2_A           97 TLYLNFVEKVQWS  109 (114)
T ss_dssp             ECEEEEESCCCCS
T ss_pred             EEEEEecccCccc
Confidence            9999999876543

>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=99.38  E-value=2.6e-13  Score=118.89  Aligned_cols=67  Identities=21%  Similarity=0.190  Sum_probs=57.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ..++|||+|||+++|+++|+++|++||.|.+|.+..+..+|+++|||||+|.+.++|.+|++.++..
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~   90 (115)
T 2cpx_A           24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGY   90 (115)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            4689999999999999999999999999954444433337999999999999999999999987654

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

Probab=99.37  E-value=1.3e-12  Score=112.00  Aligned_cols=80  Identities=23%  Similarity=0.278  Sum_probs=68.5

Q ss_pred             CCcEEEEcCCC------cCCHHHHHHHhhcCCCeeEEEEeeCCCC-CCcccEEEEEEeehhhHHHhhHHHHHHhCCeeec
Q psy15852         99 KNKMVSHPGIV------HKITEELKEHFSKYGEIENVTLKSDPNT-GRSRGFAFIVFKDTESLEKASVEDVIAEGNHVIN  171 (661)
Q Consensus        99 ~~~~~~~~~~~------~~te~~L~~~F~~~G~I~~v~l~~~~~t-g~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~  171 (661)
                      ..++|++.|+.      +-++++|+++|++||+|.+|+|++++.+ ++++|||||+|.++++|.+|    +..+|+..+.
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~A----i~~lnG~~~~   82 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKA----VVDLNGRYFG   82 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHH----HHHHTTCEET
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHH----HHHHCCCEEC
Confidence            34566666664      2378999999999999999999998764 68999999999999999999    9999999999


Q ss_pred             ceeehhhhhhc
Q psy15852        172 NKKIEAKKAKA  182 (661)
Q Consensus       172 g~~i~v~~~~~  182 (661)
                      |+.|.|.++.+
T Consensus        83 Gr~i~v~~a~~   93 (105)
T 2pe8_A           83 GRVVKACFYNL   93 (105)
T ss_dssp             TEECEEEECCH
T ss_pred             CcEEEEEEcCH
Confidence            99999987754

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

Probab=99.36  E-value=1.1e-12  Score=112.09  Aligned_cols=73  Identities=15%  Similarity=0.198  Sum_probs=64.2

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||.|.+|+++      +++|||||+|.+.++|.+|    +..+++..+.|+.|.|.+
T Consensus        28 ~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~A----i~~l~g~~~~g~~l~V~~   97 (101)
T 2la4_A           28 TTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVC----IVALANFPFQGRNLRTGW   97 (101)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHH----HHHHTTCEETTEECCCCB
T ss_pred             CEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHH----HHHhCCCeECCeEEEEEe
Confidence            344444444599999999999999999999998      3578999999999999999    889999999999999998


Q ss_pred             hhc
Q psy15852        180 AKA  182 (661)
Q Consensus       180 ~~~  182 (661)
                      +++
T Consensus        98 a~~  100 (101)
T 2la4_A           98 GKE  100 (101)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            875

>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=99.36  E-value=6.3e-13  Score=114.86  Aligned_cols=61  Identities=16%  Similarity=0.162  Sum_probs=54.8

Q ss_pred             cCCCeEEE--cCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        591 EAKNKMVS--HPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       591 ~~~~~l~v--~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      ++.++|||  +|||+++|+++|+++|++||.|.+|.|+.      .||||||+|.+.++|++|++.+|.
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG   85 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNG   85 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCC
Confidence            34678999  66999999999999999999999998874      278999999999999999998775

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

Probab=99.36  E-value=8.9e-13  Score=111.42  Aligned_cols=78  Identities=12%  Similarity=0.218  Sum_probs=70.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEE-EeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIET-EMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v-~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ..++|||+|||+++++++|+++|++||.|..| .++.++.++    .|||+|.+.++|.+|++.+ +..+.|+.|.|.++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45899999999999999999999999999999 588876543    3999999999999999965 78999999999999


Q ss_pred             cCCC
Q psy15852        261 TPKP  264 (661)
Q Consensus       261 ~~k~  264 (661)
                      .++.
T Consensus        90 ~~~~   93 (96)
T 2e44_A           90 PDEM   93 (96)
T ss_dssp             CCCC
T ss_pred             Cccc
Confidence            9874

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

Probab=99.36  E-value=7.5e-13  Score=117.63  Aligned_cols=80  Identities=18%  Similarity=0.153  Sum_probs=68.4

Q ss_pred             CCCcEEEEcCCCcCCHHHHH----HHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecce
Q psy15852         98 AKNKMVSHPGIVHKITEELK----EHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK  173 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~----~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~  173 (661)
                      +..+++|.+|++.+++++|+    ++|++||+|.+|.+.+   ++++||||||+|.+.++|.+|    +..+|+..|.|+
T Consensus        28 p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~A----i~~lng~~l~gr  100 (127)
T 2a3j_A           28 PSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAF----VEAFQGYPFQGN  100 (127)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHH----HHHSTTCCCTTS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHH----HHHHCCCEeCCC
Confidence            34455555555699999876    7999999999998864   588999999999999999999    999999999999


Q ss_pred             eehhhhhhccC
Q psy15852        174 KIEAKKAKAKS  184 (661)
Q Consensus       174 ~i~v~~~~~~~  184 (661)
                      +|.|.++..+.
T Consensus       101 ~l~V~~a~~~~  111 (127)
T 2a3j_A          101 PLVITFSETPQ  111 (127)
T ss_dssp             CCEEEECCCCC
T ss_pred             EEEEEEccCcc
Confidence            99999987654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.03  E-value=8.9e-14  Score=122.15  Aligned_cols=82  Identities=21%  Similarity=0.258  Sum_probs=72.9

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeE--------EEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeee
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIEN--------VTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVI  170 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~--------v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i  170 (661)
                      ..++++.++++++++++|+++|++||+|.+        |+|+.++.+++++|||||+|.+.++|++|    +..+++..+
T Consensus         7 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A----i~~l~g~~~   82 (116)
T 2lcw_A            7 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAA----IDWFDGKEF   82 (116)
Confidence            344555555559999999999999999999        99999988999999999999999999999    888999999


Q ss_pred             cceeehhhhhhccC
Q psy15852        171 NNKKIEAKKAKAKS  184 (661)
Q Consensus       171 ~g~~i~v~~~~~~~  184 (661)
                      .|++|.|.++.++.
T Consensus        83 ~g~~l~V~~a~~~~   96 (116)
T 2lcw_A           83 SGNPIKVSFATRRA   96 (116)
Confidence            99999999988764

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.34  E-value=1.2e-12  Score=111.76  Aligned_cols=78  Identities=23%  Similarity=0.331  Sum_probs=67.0

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..+++|.++++++++++|+++|++||.|   +++.+ .+++++|||||+|.+.++|++|    +..+++..|.|+.|.|.
T Consensus        15 ~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           15 SKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEA----LNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHH----HHHTSSEEETTEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHH----HHHhCCCEeCCeEEEEE
Confidence            3455555555599999999999999977   66776 5699999999999999999999    88899999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        87 ~a~~~~   92 (101)
T 2fc9_A           87 LQGPRG   92 (101)
T ss_dssp             ECSSCC
T ss_pred             EcCCCC
Confidence            987654

>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=99.34  E-value=1.2e-12  Score=108.79  Aligned_cols=75  Identities=13%  Similarity=0.203  Sum_probs=68.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||+++++++|+++|++| .|.+|.+.      +++|||||+|.+.++|++|++.+ +..+.|++|.|.++.
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            35789999999999999999999999 99999884      56999999999999999999976 678999999999997


Q ss_pred             CCC
Q psy15852        262 PKP  264 (661)
Q Consensus       262 ~k~  264 (661)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.34  E-value=8.9e-13  Score=114.15  Aligned_cols=77  Identities=16%  Similarity=0.124  Sum_probs=65.9

Q ss_pred             CCCcEEEEcCC-CcCCHHHHHHHhhcCC-CeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceee
Q psy15852         98 AKNKMVSHPGI-VHKITEELKEHFSKYG-EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKI  175 (661)
Q Consensus        98 ~~~~~~~~~~~-~~~te~~L~~~F~~~G-~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i  175 (661)
                      .....|+|+|+ +++++++|+++|++|| +|..|.|+.    +.++|||||+|.+.++|++|    +..+|+..+.|+.|
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~A----i~~lng~~l~Gr~i   97 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEA----LERLNNIEFRGSVI   97 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHH----HHHTTTEEETTEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHH----HHHcCCCEECCeEE
Confidence            34445555555 5999999999999999 899999864    35899999999999999999    89999999999999


Q ss_pred             hhhhhhc
Q psy15852        176 EAKKAKA  182 (661)
Q Consensus       176 ~v~~~~~  182 (661)
                      .|.++..
T Consensus        98 ~V~~a~~  104 (111)
T 2jvr_A           98 TVERDDN  104 (111)
T ss_dssp             EEEESCC
T ss_pred             EEEECCC
Confidence            9988754

>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=99.34  E-value=1.7e-12  Score=109.94  Aligned_cols=77  Identities=13%  Similarity=0.257  Sum_probs=67.8

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeec--ceee
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVIN--NKKI  175 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~--g~~i  175 (661)
                      +..++++.++++++++++|+++|++||+|.+|+++.+      +|||||+|.+.++|++|    +..+++..+.  |+.|
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A----~~~l~g~~~~~~g~~l   85 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAA----CAKMRGFPLGGPDRRL   85 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHH----HHHHTTCBCSSSSCBC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHH----HHHHCCCEeCCCCcEE
Confidence            4456666666669999999999999999999999864      68999999999999999    8889999999  9999


Q ss_pred             hhhhhhccC
Q psy15852        176 EAKKAKAKS  184 (661)
Q Consensus       176 ~v~~~~~~~  184 (661)
                      .|.++.++.
T Consensus        86 ~V~~a~~~~   94 (97)
T 1why_A           86 RVDFAKSGP   94 (97)
T ss_dssp             EEEECCCCC
T ss_pred             EEEECCCCC
Confidence            999987754

>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=99.33  E-value=2.7e-12  Score=111.02  Aligned_cols=74  Identities=22%  Similarity=0.245  Sum_probs=65.7

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecc-----ee
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN-----KK  174 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g-----~~  174 (661)
                      .+++|.+|++++++++|+++|++||+|.+|+|+.+       |||||+|.+.++|++|    +..+|+..|.|     +.
T Consensus        16 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~A----i~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYA----VRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             CEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHH----HHHSSSEEEECTTSCEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHH----HHHHCcCCccCCcCcceE
Confidence            44555555559999999999999999999999986       7999999999999999    89999999999     99


Q ss_pred             ehhhhhhccC
Q psy15852        175 IEAKKAKAKS  184 (661)
Q Consensus       175 i~v~~~~~~~  184 (661)
                      |.|.++.++.
T Consensus        85 i~V~~a~~~~   94 (108)
T 1x4c_A           85 IRVKVDGPRS   94 (108)
T ss_dssp             EEEEESSCCS
T ss_pred             EEEEeCCCCC
Confidence            9999987654

>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=99.33  E-value=2.9e-12  Score=105.58  Aligned_cols=74  Identities=20%  Similarity=0.332  Sum_probs=64.5

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHh-CCeeecceeeh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE-GNHVINNKKIE  176 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~-~~~~i~g~~i~  176 (661)
                      ...++++.++++++++++|+++|++||+|.+|++++      ++|||||+|.+.++|++|    +..+ ++..+.|++|.
T Consensus        11 ~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~------~kg~afV~f~~~~~A~~a----~~~l~~~~~~~g~~l~   80 (85)
T 2ytc_A           11 TITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ------RQQCAFIQFATRQAAEVA----AEKSFNKLIVNGRRLN   80 (85)
T ss_dssp             SCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHH----HHTTTTTCEETTEECC
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC------CCCEEEEEECCHHHHHHH----HHHhcCCeeECCCEEE
Confidence            345566666666999999999999999999999997      378999999999999998    8878 99999999999


Q ss_pred             hhhhh
Q psy15852        177 AKKAK  181 (661)
Q Consensus       177 v~~~~  181 (661)
                      |.+++
T Consensus        81 v~~ak   85 (85)
T 2ytc_A           81 VKWGR   85 (85)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            98763

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

Probab=99.33  E-value=2.3e-12  Score=107.54  Aligned_cols=74  Identities=18%  Similarity=0.300  Sum_probs=64.8

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|.+|+|+        +|||||+|.+.++|++|    +..+++..+.|++|.|.
T Consensus         8 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l~v~   75 (90)
T 2dnq_A            8 MVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDA----IRNLHHYKLHGVNINVE   75 (90)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHH----HHHHTTCBCSSCBCEEE
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHH----HHHhcCCccCCcEEEEE
Confidence            3445555555599999999999999999999998        57999999999999999    88999999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        76 ~a~~~~   81 (90)
T 2dnq_A           76 ASKNKS   81 (90)
T ss_dssp             CSSCCC
T ss_pred             ECCCCC
Confidence            987654

>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=99.33  E-value=2.2e-12  Score=111.81  Aligned_cols=76  Identities=22%  Similarity=0.415  Sum_probs=66.5

Q ss_pred             CCcEEEEcCC-CcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         99 KNKMVSHPGI-VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        99 ~~~~~~~~~~-~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ..+.||++|+ +++++++|+++|++||+|.+|+|+++      +|||||+|.+.++|++|    +..+++..|.|+.|.|
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~v   93 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHA----IVSVNGTTIEGHVVKC   93 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHH----HHHHTTCEETTEECEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHH----HHHcCCCEECCcEEEE
Confidence            3444555555 59999999999999999999999985      78999999999999999    8899999999999999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .++.++.
T Consensus        94 ~~a~~~~  100 (109)
T 1x4g_A           94 YWGKESP  100 (109)
T ss_dssp             ECCCCCC
T ss_pred             EecCCCC
Confidence            9987654

>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=99.33  E-value=6e-13  Score=110.55  Aligned_cols=58  Identities=28%  Similarity=0.454  Sum_probs=53.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|+++     ++|||||+|.+.++|++|+..
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~   61 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE   61 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC
Confidence            3589999999999999999999999999999999965     789999999999999987654

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

Probab=99.33  E-value=2e-12  Score=110.55  Aligned_cols=80  Identities=26%  Similarity=0.331  Sum_probs=70.6

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ...++++.++++++++++|+++|+.|+   +|+++.++.+++++|||||+|.+.++|++|    +..+++..|.|+.|.|
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l~V   86 (102)
T 2fc8_A           14 PSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAA----KEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             CCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHH----HHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHH----HHHhCCCeECCeEEEE
Confidence            445666666666999999999999873   788899888899999999999999999999    8889999999999999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .++.++.
T Consensus        87 ~~a~~~~   93 (102)
T 2fc8_A           87 DWAKPKG   93 (102)
T ss_dssp             EECCCCC
T ss_pred             EEecCCC
Confidence            9987754

>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=99.33  E-value=1.3e-12  Score=114.51  Aligned_cols=59  Identities=19%  Similarity=0.196  Sum_probs=54.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      .++|||.|||+++|++||+++|++||.|.+|+|+.+       |||||+|.+.++|.+||++++..
T Consensus        16 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~   74 (115)
T 3beg_B           16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNT   74 (115)
T ss_dssp             -CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCC
Confidence            578999999999999999999999999999999976       89999999999999999986654

>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=99.32  E-value=3.1e-12  Score=117.53  Aligned_cols=77  Identities=10%  Similarity=0.109  Sum_probs=68.5

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC--eEEEEEecc
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND--KEVDVKKAT  261 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g--~~i~V~~a~  261 (661)
                      .+|||+||++.+++++|+++|++||+|.+|.|..+    .++|||||+|.+.++|.+|++.+ +..|.|  +.|+|.|++
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            57899999999999999999999999999998653    25889999999999999999987 677855  999999999


Q ss_pred             CCCC
Q psy15852        262 PKPE  265 (661)
Q Consensus       262 ~k~~  265 (661)
                      ++..
T Consensus       123 ~~~l  126 (164)
T 1sjr_A          123 LTSL  126 (164)
T ss_dssp             SSSC
T ss_pred             CCcc
Confidence            8653

>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=99.32  E-value=1.2e-12  Score=110.77  Aligned_cols=80  Identities=24%  Similarity=0.351  Sum_probs=69.8

Q ss_pred             CCCcEEEEcCCCcCCHHHHH----HHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecce
Q psy15852         98 AKNKMVSHPGIVHKITEELK----EHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK  173 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~----~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~  173 (661)
                      +..++++.++++++++++|+    ++|++||+|.+|++++   ++.++|||||+|.+.++|.+|    +..+++..+.|+
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A----~~~l~g~~~~g~   79 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA----LRSMQGFPFYDK   79 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHH----HHHHTTCEETTE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHH----HHHhCCCEECCc
Confidence            34555555555699999999    9999999999999984   478999999999999999999    889999999999


Q ss_pred             eehhhhhhccC
Q psy15852        174 KIEAKKAKAKS  184 (661)
Q Consensus       174 ~i~v~~~~~~~  184 (661)
                      .|.|.++.++.
T Consensus        80 ~l~v~~a~~~~   90 (97)
T 1nu4_A           80 PMRIQYAKTDS   90 (97)
T ss_dssp             ECEEEECSSCC
T ss_pred             EEEEEEccCCC
Confidence            99999987654

>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=99.32  E-value=1.8e-12  Score=110.22  Aligned_cols=77  Identities=22%  Similarity=0.351  Sum_probs=67.4

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      +..++++.++++++++++|+++|++||+|.+|+|+++      +|||||+|.+.++|++|    +..+++..+.|++|.|
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a----~~~l~g~~~~g~~l~v   83 (99)
T 2cpj_A           14 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIA----KVELDNMPLRGKQLRV   83 (99)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHH----HHHHTTCCBTTBCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHH----HHHhCCCEeCCceEEE
Confidence            3445556556669999999999999999999999864      68999999999999999    8899999999999999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .++.++.
T Consensus        84 ~~a~~~~   90 (99)
T 2cpj_A           84 RFACHSA   90 (99)
T ss_dssp             EESSCCS
T ss_pred             EEcCCCC
Confidence            9988754

>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=99.32  E-value=3.7e-13  Score=122.83  Aligned_cols=83  Identities=18%  Similarity=0.304  Sum_probs=70.2

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEE--eccC---CCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEE
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETE--MPYD---KSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVD  256 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~--i~~~---~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~  256 (661)
                      ..++|||+|||+.+++++|+++|++||.|..+.  ++.+   ..+++++|||||+|.+.++|.+|++.+ +..+.|+.|.
T Consensus        44 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~  123 (143)
T 3egn_A           44 PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMV  123 (143)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            457999999999999999999999999987641  1111   235889999999999999999999975 6899999999


Q ss_pred             EEeccCCCC
Q psy15852        257 VKKATPKPE  265 (661)
Q Consensus       257 V~~a~~k~~  265 (661)
                      |.++.+...
T Consensus       124 V~~a~~~~~  132 (143)
T 3egn_A          124 VQFARSARP  132 (143)
T ss_dssp             EEECCCSCC
T ss_pred             EEECCCCCC
Confidence            999987543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.31  E-value=1.6e-13  Score=117.21  Aligned_cols=79  Identities=24%  Similarity=0.252  Sum_probs=68.7

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||.|.+ .++.++.+++++|||||+|.+.++|++|    +. +++..+.|+.|.|.+
T Consensus        18 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A----~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           18 FNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKA----LE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHH----HH-GGGCCBTTBCCEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHH----Hh-cCCcEECCcEEEEEE
Confidence            44555555559999999999999999988 7777777899999999999999999998    76 999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        92 a~~~~   96 (101)
T 1fj7_A           92 PKGRD   96 (101)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            87654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.31  E-value=4.8e-12  Score=111.94  Aligned_cols=76  Identities=12%  Similarity=0.163  Sum_probs=68.1

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcE-EEEEeCCHHHHHHHHHhC-CCccCC--eEEEEEec
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF-CFITFEHESVVIDLLKNP-KQKIND--KEVDVKKA  260 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~-afV~f~~~~~A~~Al~~~-~~~~~g--~~i~V~~a  260 (661)
                      -+|||+||++.+|+++|+++|++||.|.+|.++.+     .+|| |||+|.+.++|.+|++.+ +..|.|  +.|+|.++
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~a  103 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  103 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEEC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEec
Confidence            46889999999999999999999999999988753     3688 999999999999999997 678887  99999999


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      +++.-
T Consensus       104 k~~~l  108 (130)
T 3zzy_A          104 KLTSL  108 (130)
T ss_dssp             SCSSC
T ss_pred             CCCce
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=99.31  E-value=3.9e-12  Score=122.06  Aligned_cols=64  Identities=19%  Similarity=0.252  Sum_probs=60.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      .++|||+|||+++|+++|+++|++||.|.+|+|++++. |+++|||||+|.+.++|.+|++..++
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~-~~~kG~aFVeF~~~e~A~~A~~~~~~  172 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQ  172 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTT-CCEEEEEEEEESSHHHHHHHHHCTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCC-CCcccEEEEEECCHHHHHHHHHhCCC
Confidence            47899999999999999999999999999999999875 99999999999999999999987654

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

Probab=99.30  E-value=6.2e-12  Score=103.05  Aligned_cols=73  Identities=10%  Similarity=0.151  Sum_probs=64.3

Q ss_pred             CCe-eEecCCCccCCHHH----HHHHHhcC-CCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEE
Q psy15852        184 SGK-IFVGGLSPEMKDEE----IKAHFAQF-GNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVD  256 (661)
Q Consensus       184 ~~~-lfV~nLp~~~te~~----L~~~F~~~-G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~  256 (661)
                      ..+ |||+|||+.+++++    |+++|++| |+|.+|       ++   |+|||+|.+.++|.+|++.+ +..+.||+|+
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            445 99999999999987    55899999 499988       23   99999999999999999986 7899999999


Q ss_pred             EEeccCCCCC
Q psy15852        257 VKKATPKPEP  266 (661)
Q Consensus       257 V~~a~~k~~~  266 (661)
                      |.+|+.+.+-
T Consensus        78 v~~A~~~sd~   87 (96)
T 2diu_A           78 VSFTPKNREL   87 (96)
T ss_dssp             EESSCCSCCC
T ss_pred             EEecCCCcce
Confidence            9999987653

>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=99.30  E-value=4.9e-12  Score=104.63  Aligned_cols=71  Identities=15%  Similarity=0.406  Sum_probs=64.2

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcC----C-------CeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQF----G-------NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKIN  251 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~----G-------~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~  251 (661)
                      ..++|||+|||+++++++|+++|++|    |       .|.++.+.++      +|||||+|.+.++|.+|+..++..++
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~~l~g~~~~   78 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAMAFDGIIFQ   78 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHGGGTTCEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHHhcCCCEEC
Confidence            45799999999999999999999999    8       9999999654      89999999999999999944478999


Q ss_pred             CeEEEEEe
Q psy15852        252 DKEVDVKK  259 (661)
Q Consensus       252 g~~i~V~~  259 (661)
                      |+.|.|+.
T Consensus        79 g~~l~V~r   86 (87)
T 2hzc_A           79 GQSLKIRR   86 (87)
T ss_dssp             TEECEEEC
T ss_pred             CeEEEEeC
Confidence            99999974

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

Probab=99.30  E-value=8.4e-12  Score=107.02  Aligned_cols=82  Identities=11%  Similarity=0.103  Sum_probs=71.4

Q ss_pred             ccCCeeEecCCCc-----cCCHHHHHHHHhcCCCeEEEEeccCCCC-CCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeE
Q psy15852        182 AKSGKIFVGGLSP-----EMKDEEIKAHFAQFGNIIETEMPYDKSK-SQRKNFCFITFEHESVVIDLLKNP-KQKINDKE  254 (661)
Q Consensus       182 ~~~~~lfV~nLp~-----~~te~~L~~~F~~~G~i~~v~i~~~~~~-g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~  254 (661)
                      ..+++|+|+||..     +.++++|+++|++||+|.+|.|++++.+ ++++|||||+|.+.++|.+|++.+ +..+.||.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4568999999963     2478999999999999999999988654 688999999999999999999986 68999999


Q ss_pred             EEEEeccCC
Q psy15852        255 VDVKKATPK  263 (661)
Q Consensus       255 i~V~~a~~k  263 (661)
                      |.|.++...
T Consensus        86 i~v~~a~~~   94 (105)
T 2pe8_A           86 VKACFYNLD   94 (105)
T ss_dssp             CEEEECCHH
T ss_pred             EEEEEcCHH
Confidence            999998753

>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=99.30  E-value=4e-12  Score=108.94  Aligned_cols=76  Identities=22%  Similarity=0.291  Sum_probs=66.5

Q ss_pred             cCCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852         97 EAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus        97 ~~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      .+..+++|.++++++++++|+++|++||+|.+|+|++        |||||+|.+.++|++|    +..+++..|.|+.|.
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~   76 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKA----MEEMNGKDLEGENIE   76 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHH----HHHHTTEEETTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHH----HHHHCCCccCCCEEE
Confidence            3445666666666999999999999999999999874        4999999999999999    888999999999999


Q ss_pred             hhhhhccC
Q psy15852        177 AKKAKAKS  184 (661)
Q Consensus       177 v~~~~~~~  184 (661)
                      |.++.++.
T Consensus        77 v~~a~~~~   84 (103)
T 2dgu_A           77 IVFAKPPD   84 (103)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCc
Confidence            99987654

>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=99.30  E-value=5.6e-12  Score=106.72  Aligned_cols=75  Identities=24%  Similarity=0.376  Sum_probs=65.8

Q ss_pred             cCCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceee
Q psy15852         97 EAKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKI  175 (661)
Q Consensus        97 ~~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i  175 (661)
                      ....++++.++++ ++++++|+++|++||.|.+|+|.        +|||||+|.+.++|.+|    +..+++..+.|+.|
T Consensus        20 ~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A----i~~l~g~~~~g~~l   87 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDA----IEXESQEMNFGKKL   87 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHH----HHHHTTSEETTEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHH----HHHcCCCEECCEEE
Confidence            3455666666666 89999999999999999999983        68999999999999999    88899999999999


Q ss_pred             hhhhhhcc
Q psy15852        176 EAKKAKAK  183 (661)
Q Consensus       176 ~v~~~~~~  183 (661)
                      .|.++.++
T Consensus        88 ~V~~a~~~   95 (97)
T 2xnq_A           88 ILEVSSSN   95 (97)
T ss_dssp             EEEECCCC
T ss_pred             EEEecCCC
Confidence            99988764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.29  E-value=7e-12  Score=106.15  Aligned_cols=74  Identities=19%  Similarity=0.352  Sum_probs=65.7

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .+.||++|+ ++++++|+++|++||+|.+|+|.      +++|||||+|.+.++|++|    +..+++..+.|++|.|.+
T Consensus        15 ~~~l~V~n~-~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~A----i~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           15 GNTLYVYGE-DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQA----VAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CSEEEEECS-SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHH----HHHTTTEEETTEEEEEEC
T ss_pred             CCEEEEcCC-CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHH----HHHhCCCeECCeEEEEEE
Confidence            455666664 99999999999999999999995      4688999999999999999    889999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        84 a~~~~   88 (97)
T 1x5p_A           84 ARKQP   88 (97)
T ss_dssp             CSSCC
T ss_pred             CCCCC
Confidence            87654

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

Probab=99.29  E-value=4.4e-12  Score=109.67  Aligned_cols=75  Identities=25%  Similarity=0.372  Sum_probs=66.2

Q ss_pred             CCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852         98 AKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus        98 ~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ...+.||++|+| ++++++|+++|++||+|.+|+|+        +|||||+|.+.++|++|    +..+++..+.|+.|.
T Consensus        29 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~A----i~~l~g~~~~g~~l~   96 (108)
T 2jvo_A           29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKA----IEEVHGKSFANQPLE   96 (108)
T ss_dssp             CSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHH----HHHHTTCEETTEECE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHH----HHHcCCCEECCeEEE
Confidence            344556666665 99999999999999999999998        68999999999999999    889999999999999


Q ss_pred             hhhhhccC
Q psy15852        177 AKKAKAKS  184 (661)
Q Consensus       177 v~~~~~~~  184 (661)
                      |.++.++.
T Consensus        97 V~~a~~~~  104 (108)
T 2jvo_A           97 VVYSKLPA  104 (108)
T ss_dssp             EESCSCCC
T ss_pred             EEEecCCC
Confidence            99987654

>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=99.29  E-value=1.6e-12  Score=113.00  Aligned_cols=73  Identities=16%  Similarity=0.211  Sum_probs=64.4

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+.||++|+| ++++++|+++|++||+|.+|.|+.      ++|||||+|.+.++|++|    +..+|+..+.|+.|.|.
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~A----i~~l~g~~~~g~~l~V~   79 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKA----FRHLAYSKFHHVPLYLE   79 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHH----HHHHTTCBSSSSBCEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHH----HHHhCCCEECCeEEEEE
Confidence            3455555555 999999999999999999999874      578999999999999999    99999999999999999


Q ss_pred             hhhc
Q psy15852        179 KAKA  182 (661)
Q Consensus       179 ~~~~  182 (661)
                      ++..
T Consensus        80 ~a~~   83 (111)
T 1whx_A           80 WAPI   83 (111)
T ss_dssp             EEET
T ss_pred             ECCC
Confidence            9875

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.29  E-value=2.2e-12  Score=109.29  Aligned_cols=77  Identities=14%  Similarity=0.182  Sum_probs=66.2

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++||+|. ++++.    ++++|||||+|.+.++|++|    +..+|+..+.|+.|.|.
T Consensus        19 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~V~   89 (97)
T 2e5j_A           19 AADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQA----VSCLQGLRLGTDTLRVA   89 (97)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHH----HHHHTTCCSSSSCCEEE
T ss_pred             CCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHH----HHHhCCCEECCcEEEEE
Confidence            34555555555999999999999999997 77775    46899999999999999999    88999999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        90 ~a~~~~   95 (97)
T 2e5j_A           90 LARQQR   95 (97)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            987654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.27  E-value=2.2e-12  Score=109.00  Aligned_cols=76  Identities=25%  Similarity=0.348  Sum_probs=65.1

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||.|..+     ..+++++|||||+|.+.++|.+|    +..+++..+.|+.|.|.+
T Consensus        17 ~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           17 RTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKN----LEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             GEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHH----HHHTTEEEETTEEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHH----HHHhCCCEECCeEEEEEE
Confidence            445555555599999999999999988766     34589999999999999999999    888999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        88 a~~~~   92 (96)
T 1fjc_A           88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             cCCCC
Confidence            87654

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

Probab=99.27  E-value=4.8e-12  Score=103.70  Aligned_cols=77  Identities=16%  Similarity=0.152  Sum_probs=66.9

Q ss_pred             ecCCCcEEEEcCCC-cCCHHH----HHHHhhcC-CCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCee
Q psy15852         96 MEAKNKMVSHPGIV-HKITEE----LKEHFSKY-GEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV  169 (661)
Q Consensus        96 ~~~~~~~~~~~~~~-~~te~~----L~~~F~~~-G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~  169 (661)
                      .++..++|||+|+| .+++++    |+++|++| |+|.+|       |+   |+|||.|.+.++|.+|    +..+++..
T Consensus         5 ~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A----~~~l~G~~   70 (96)
T 2diu_A            5 SSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERA----QKRMENED   70 (96)
T ss_dssp             CCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHH----HHHHTTCC
T ss_pred             CCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHH----HHHhcCCc
Confidence            34567779888888 999888    55899999 599988       34   9999999999999999    99999999


Q ss_pred             ecceeehhhhhhccCCe
Q psy15852        170 INNKKIEAKKAKAKSGK  186 (661)
Q Consensus       170 i~g~~i~v~~~~~~~~~  186 (661)
                      +.||+|.|.+++.++.-
T Consensus        71 l~gr~i~v~~A~~~sd~   87 (96)
T 2diu_A           71 VFGNRIIVSFTPKNREL   87 (96)
T ss_dssp             SSSSCCEEESSCCSCCC
T ss_pred             cCCceEEEEecCCCcce
Confidence            99999999999876643

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.27  E-value=1.2e-11  Score=108.92  Aligned_cols=74  Identities=8%  Similarity=0.044  Sum_probs=65.6

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcE-EEEEeCCHHHHHHHHHhC-CCccCC--eEEEEEecc
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF-CFITFEHESVVIDLLKNP-KQKIND--KEVDVKKAT  261 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~-afV~f~~~~~A~~Al~~~-~~~~~g--~~i~V~~a~  261 (661)
                      .|||+||++.+++++|+++|++||.|.+|.|...      .|| |||+|.+.++|.+|++.+ +..|.|  +.|+|.++.
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            5789999999999999999999999999998642      386 999999999999999986 678877  699999998


Q ss_pred             CCCC
Q psy15852        262 PKPE  265 (661)
Q Consensus       262 ~k~~  265 (661)
                      ++..
T Consensus       101 ~~~l  104 (124)
T 2e5i_A          101 PTRL  104 (124)
T ss_dssp             CSCC
T ss_pred             CCcc
Confidence            7653

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

Probab=99.27  E-value=5.3e-12  Score=106.67  Aligned_cols=76  Identities=24%  Similarity=0.381  Sum_probs=66.0

Q ss_pred             cCCCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceee
Q psy15852         97 EAKNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKI  175 (661)
Q Consensus        97 ~~~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i  175 (661)
                      ++..++++.++++ ++++++|+++|++||+|.+|+|.        +|||||+|.+.++|++|    +..+++..+.|++|
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l   75 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDA----IECESQEMNFGKKL   75 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHH----HHHHTCSSCBTTTB
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHH----HHHcCCCeeCCcEE
Confidence            3445666666666 89999999999999999999994        68999999999999999    88899999999999


Q ss_pred             hhhhhhccC
Q psy15852        176 EAKKAKAKS  184 (661)
Q Consensus       176 ~v~~~~~~~  184 (661)
                      .|.++.++.
T Consensus        76 ~V~~a~~~~   84 (96)
T 2kvi_A           76 ILEVSSSNA   84 (96)
T ss_dssp             CEEEEECCC
T ss_pred             EEEEcCcCC
Confidence            999987643

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

Probab=99.26  E-value=9.5e-12  Score=104.17  Aligned_cols=73  Identities=18%  Similarity=0.315  Sum_probs=64.1

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+|+|+++        ||||+|.+.++|++|    +..+++..+.|+.|.|.+
T Consensus        11 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~--------~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A           11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEA----IRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             EEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHH----HHHHTTEEETTEEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHH----HHHhCCCeeCCcEEEEEE
Confidence            44555555559999999999999999999999853        999999999999999    889999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        79 a~~~~   83 (92)
T 2dgt_A           79 STSRL   83 (92)
T ss_dssp             SSCCC
T ss_pred             ccCCC
Confidence            87654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.26  E-value=1.3e-11  Score=103.71  Aligned_cols=75  Identities=17%  Similarity=0.288  Sum_probs=63.4

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+|  +.++.+++   ||||+|.+.++|++|    +. +++..|.|+.|.|.+
T Consensus         9 ~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~a----i~-l~g~~~~g~~l~V~~   78 (94)
T 2e5g_A            9 RSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAV----LS-QSQHSLGGHRLRVRP   78 (94)
T ss_dssp             CEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHH----HT-CSCCEETTEECCCBC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHH----Hh-cCCeEECCEEEEEEE
Confidence            455555555599999999999999999987  55566565   999999999999998    77 999999999999998


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        79 a~~~~   83 (94)
T 2e5g_A           79 REQKE   83 (94)
T ss_dssp             SCCSC
T ss_pred             CCcCC
Confidence            86543

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

Probab=99.25  E-value=1.4e-11  Score=104.66  Aligned_cols=75  Identities=23%  Similarity=0.347  Sum_probs=64.5

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcC--CCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceee
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKY--GEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKI  175 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~--G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i  175 (661)
                      ...++++.++++++++++|+++|++|  |.|.+|+++        +|||||+|.+.++|++|    +..+++..|.|+.|
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A----~~~l~g~~~~g~~l   81 (99)
T 2cpd_A           14 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEA----MKALNGKVLDGSPI   81 (99)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHH----HHHHSSEEETTEEE
T ss_pred             CcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHH----HHHhCCCEeCCcEE
Confidence            34455555555599999999999999  899999875        46999999999999999    88899999999999


Q ss_pred             hhhhhhccC
Q psy15852        176 EAKKAKAKS  184 (661)
Q Consensus       176 ~v~~~~~~~  184 (661)
                      .|.++.++.
T Consensus        82 ~v~~a~~~~   90 (99)
T 2cpd_A           82 EVTLAKPVD   90 (99)
T ss_dssp             EEECCCCCC
T ss_pred             EEEECCCCC
Confidence            999987654

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

Probab=99.25  E-value=1.1e-11  Score=103.37  Aligned_cols=75  Identities=15%  Similarity=0.255  Sum_probs=65.6

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ...++++.++++++++++|+++|++||+|.+|+|+++        ||||+|.+.++|++|    +..+++..+.|+.|.|
T Consensus         8 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A----~~~l~g~~~~g~~l~v   75 (90)
T 2dnp_A            8 NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAA----IAQLNGKEVKGKRINV   75 (90)
T ss_dssp             CSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHH----HHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHH----HHHhCCCEECCcEEEE
Confidence            3455666666669999999999999999999999853        999999999999999    8899999999999999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .++.+..
T Consensus        76 ~~a~~~~   82 (90)
T 2dnp_A           76 ELSTKGQ   82 (90)
T ss_dssp             EESCCCC
T ss_pred             EECCCCC
Confidence            9987653

>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=99.25  E-value=7.4e-12  Score=114.98  Aligned_cols=76  Identities=17%  Similarity=0.199  Sum_probs=66.9

Q ss_pred             cEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecc--eeehh
Q psy15852        101 KMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN--KKIEA  177 (661)
Q Consensus       101 ~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g--~~i~v  177 (661)
                      ..|||+|++ .+++++|+++|++||+|.+|+|..+    +++|||||+|.+.++|++|    +..+++..|.|  ++|.|
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~A----i~~LnG~~i~g~g~~L~V  118 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHA----KLSLDGQNIYNACCTLRI  118 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHH----HHHSTTBCSSSSCSCEEE
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHH----HHHhCCCEecCCCcEEEE
Confidence            346677766 9999999999999999999999753    3689999999999999999    99999999966  99999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .+++++.
T Consensus       119 ~~Ak~~~  125 (164)
T 1sjr_A          119 DFSKLTS  125 (164)
T ss_dssp             EECSSSS
T ss_pred             EEecCCc
Confidence            9998764

>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=99.24  E-value=8.7e-12  Score=108.18  Aligned_cols=71  Identities=20%  Similarity=0.412  Sum_probs=62.9

Q ss_pred             cEEEEcCCC-c-CCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        101 KMVSHPGIV-H-KITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       101 ~~~~~~~~~-~-~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      +.||++++| + +++++|+++|++||+|.+|+|        ++|||||+|.+.++|++|    +..+++..+.|+.|.|.
T Consensus        28 ~~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           28 SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAA----VLGENGRVLAGQTLDIN   95 (110)
T ss_dssp             SEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHH----HHHHTTCEETTEECCEE
T ss_pred             cEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHH----HHHcCCCEECCeEEEEE
Confidence            455555555 8 999999999999999999999        578999999999999999    88999999999999999


Q ss_pred             hhhcc
Q psy15852        179 KAKAK  183 (661)
Q Consensus       179 ~~~~~  183 (661)
                      ++.++
T Consensus        96 ~a~~~  100 (110)
T 1wf1_A           96 MAGEP  100 (110)
T ss_dssp             ESCCC
T ss_pred             ECCCC
Confidence            98743

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.24  E-value=2.4e-11  Score=106.94  Aligned_cols=58  Identities=12%  Similarity=0.129  Sum_probs=52.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccE-EEEEEcCHHHHHHHHHhCCcc
Q psy15852        595 KMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGF-AFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       595 ~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~-aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      .|||.|||+.+|+++|+++|++||.|.+|+|+..      +|| |||+|.+.++|.+|++.++.+
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~   85 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGA   85 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCC
Confidence            5789999999999999999999999999999752      286 999999999999999987654

>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=99.24  E-value=9.7e-12  Score=103.21  Aligned_cols=74  Identities=11%  Similarity=0.183  Sum_probs=65.5

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++++++|+++|++| +|.+|+|.      +++|||||+|.++++|++|    +..+++..+.|++|.|.
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~A----i~~l~g~~~~g~~l~V~   73 (88)
T 1wg1_A            5 SSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNA----IQMFHQYSFRGKDLIVQ   73 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHH----HHHHTTEEETTEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHH----HHHhCCCeECCcEEEEE
Confidence            3556666666699999999999999 99999985      5799999999999999999    88999999999999999


Q ss_pred             hhhcc
Q psy15852        179 KAKAK  183 (661)
Q Consensus       179 ~~~~~  183 (661)
                      ++...
T Consensus        74 ~a~~~   78 (88)
T 1wg1_A           74 LQPTD   78 (88)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            88653

>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=99.24  E-value=9.8e-12  Score=134.17  Aligned_cols=80  Identities=16%  Similarity=0.395  Sum_probs=71.6

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .+|||.+|++.+|+++|+++|++||+|..|.|+.++.+++++|||||+|.+.++|.+|    +..+|+..|.|+.|.|.+
T Consensus       103 ~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~A----i~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S          103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA----YKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHH----HHHcCCCEECCEEEEEEE
Confidence            3444444445999999999999999999999999998999999999999999999999    889999999999999988


Q ss_pred             hhcc
Q psy15852        180 AKAK  183 (661)
Q Consensus       180 ~~~~  183 (661)
                      +.+.
T Consensus       179 a~~~  182 (437)
T 3pgw_S          179 ERGR  182 (437)
T ss_pred             eCCC
Confidence            7753

>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=99.23  E-value=6e-12  Score=105.61  Aligned_cols=76  Identities=17%  Similarity=0.217  Sum_probs=65.0

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCC-eeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCC-eeecceee
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGE-IENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGN-HVINNKKI  175 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~-I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~-~~i~g~~i  175 (661)
                      ...++++.++++++++++|+++|++||. |..+.+.       ++|||||+|.+.++|++|    +..+++ ..+.|+.|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A----~~~l~g~~~~~g~~l   75 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRA----IETLSGKVELHGKIM   75 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHH----HHHHTTTCEETTEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHH----HHHccCCeeECCEEE
Confidence            3456666666669999999999999999 6666663       578999999999999999    889999 99999999


Q ss_pred             hhhhhhccC
Q psy15852        176 EAKKAKAKS  184 (661)
Q Consensus       176 ~v~~~~~~~  184 (661)
                      .|.++.++.
T Consensus        76 ~v~~a~~~~   84 (93)
T 2cqh_A           76 EVDYSVSKK   84 (93)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCcc
Confidence            999987654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.23  E-value=1.6e-11  Score=108.61  Aligned_cols=74  Identities=19%  Similarity=0.269  Sum_probs=65.5

Q ss_pred             EEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccE-EEEEEeehhhHHHhhHHHHHHhCCeeecc--eeehh
Q psy15852        102 MVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGF-AFIVFKDTESLEKASVEDVIAEGNHVINN--KKIEA  177 (661)
Q Consensus       102 ~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~-afV~F~~~e~A~~A~~~~~~~~~~~~i~g--~~i~v  177 (661)
                      .||++|++ .+|+++|+++|++||+|.+|+|+.+     ++|| |||+|.+.++|++|    +..+||..|.|  +.|+|
T Consensus        30 ~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~A----i~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHA----KLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHH----HHHHTTCEEETTEEEEEE
T ss_pred             EEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHH----HHHcCCCeecCCCcEEEE
Confidence            45566665 9999999999999999999999863     3688 99999999999999    99999999988  89999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .++++..
T Consensus       101 ~~ak~~~  107 (130)
T 3zzy_A          101 DFSKLTS  107 (130)
T ss_dssp             EECSCSS
T ss_pred             EecCCCc
Confidence            9998764

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

Probab=99.22  E-value=1.1e-11  Score=104.73  Aligned_cols=78  Identities=14%  Similarity=0.178  Sum_probs=67.8

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEE-EEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENV-TLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v-~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ...++++.++++++++++|+++|++||+|.+| .|+.++.++    .|||+|.+.++|++|    +..+++..+.|++|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~A----i~~l~g~~~~g~~l~   85 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQA----LDKLNGFQLENFTLK   85 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHH----HHHHTTCBCSSCBCE
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHH----HHHhCCCEECCcEEE
Confidence            34566777677799999999999999999999 488876543    399999999999999    889999999999999


Q ss_pred             hhhhhcc
Q psy15852        177 AKKAKAK  183 (661)
Q Consensus       177 v~~~~~~  183 (661)
                      |.++.++
T Consensus        86 V~~a~~~   92 (96)
T 2e44_A           86 VAYIPDE   92 (96)
T ss_dssp             EEECCCC
T ss_pred             EEEcCcc
Confidence            9988765

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.22  E-value=2.2e-11  Score=119.43  Aligned_cols=95  Identities=20%  Similarity=0.275  Sum_probs=75.3

Q ss_pred             CCeeecceeehhhhh---------hccCCeeEecCCCccC---------CHHHHHHHHhcCCCeEEEEeccCCCCCCcCc
Q psy15852        166 GNHVINNKKIEAKKA---------KAKSGKIFVGGLSPEM---------KDEEIKAHFAQFGNIIETEMPYDKSKSQRKN  227 (661)
Q Consensus       166 ~~~~i~g~~i~v~~~---------~~~~~~lfV~nLp~~~---------te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g  227 (661)
                      +...+.|+.......         ....++|||+||+..+         ++++|+++|++||+|.+|.|+.      ++|
T Consensus       107 ~~~D~fGr~k~~~~~d~~~g~gs~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG  180 (240)
T 3u1l_A          107 EVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKN  180 (240)
T ss_dssp             SSBCTTSSBCGGGTC---------CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGT
T ss_pred             cCcccccchhcccchhcccCcCccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCC
Confidence            445555665544332         2345899999999998         7999999999999999999975      489


Q ss_pred             EEEEEeCCHHHHHHHHHhC-CCcc------------CCeEEEEEeccCCCCC
Q psy15852        228 FCFITFEHESVVIDLLKNP-KQKI------------NDKEVDVKKATPKPEP  266 (661)
Q Consensus       228 ~afV~f~~~~~A~~Al~~~-~~~~------------~g~~i~V~~a~~k~~~  266 (661)
                      ||||+|.+.++|++|++.+ +..|            .|+.|.|+||.+.+.+
T Consensus       181 ~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          181 CGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             EEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC-----
T ss_pred             EEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCCCCH
Confidence            9999999999999999987 5777            8999999999887654

>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=99.20  E-value=3.3e-12  Score=116.54  Aligned_cols=79  Identities=22%  Similarity=0.298  Sum_probs=66.7

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEE--------EEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCee
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENV--------TLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV  169 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v--------~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~  169 (661)
                      +..+++|.++++++++++|+++|++||.|.+|        ++.   .+++++|||||+|.+.++|.+|    +..+|+..
T Consensus        44 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~---~~g~~~g~afV~f~~~~~A~~A----i~~lng~~  116 (143)
T 3egn_A           44 PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM---KEGRMKGQAFIGLPNEKAAAKA----LKEANGYV  116 (143)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE---EETTTEEEEEEECSSHHHHHHH----HHHHTTBE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec---cCCCcccEEEEEeCCHHHHHHH----HHHhCCCE
Confidence            44455555555699999999999999998774        333   3589999999999999999999    88999999


Q ss_pred             ecceeehhhhhhcc
Q psy15852        170 INNKKIEAKKAKAK  183 (661)
Q Consensus       170 i~g~~i~v~~~~~~  183 (661)
                      |.|+.|.|.++.+.
T Consensus       117 ~~g~~l~V~~a~~~  130 (143)
T 3egn_A          117 LFGKPMVVQFARSA  130 (143)
T ss_dssp             ETTEECEEEECCCS
T ss_pred             eCCcEEEEEECCCC
Confidence            99999999988653

>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=99.17  E-value=3.2e-11  Score=99.65  Aligned_cols=70  Identities=16%  Similarity=0.339  Sum_probs=60.8

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcC----C-------CeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCC
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKY----G-------EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGN  167 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~----G-------~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~  167 (661)
                      .+++++.++++++++++|+++|++|    |       +|.+|++.++      +|||||+|.++++|.+|    + .+++
T Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A----~-~l~g   74 (87)
T 2hzc_A            6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQA----M-AFDG   74 (87)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHH----G-GGTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHH----H-hcCC
Confidence            3455555555699999999999999    8       9999999864      78999999999999998    8 9999


Q ss_pred             eeecceeehhhh
Q psy15852        168 HVINNKKIEAKK  179 (661)
Q Consensus       168 ~~i~g~~i~v~~  179 (661)
                      ..+.|+.|.|.+
T Consensus        75 ~~~~g~~l~V~r   86 (87)
T 2hzc_A           75 IIFQGQSLKIRR   86 (87)
T ss_dssp             CEETTEECEEEC
T ss_pred             CEECCeEEEEeC
Confidence            999999998864

>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=99.14  E-value=1.1e-10  Score=100.13  Aligned_cols=81  Identities=14%  Similarity=0.219  Sum_probs=69.1

Q ss_pred             cCCeeEecCC--CccCC--------HHHHHHHHhcCCCeEEEEeccCCCC--CCcCcEEEEEeCCHHHHHHHHHhC-CCc
Q psy15852        183 KSGKIFVGGL--SPEMK--------DEEIKAHFAQFGNIIETEMPYDKSK--SQRKNFCFITFEHESVVIDLLKNP-KQK  249 (661)
Q Consensus       183 ~~~~lfV~nL--p~~~t--------e~~L~~~F~~~G~i~~v~i~~~~~~--g~~~g~afV~f~~~~~A~~Al~~~-~~~  249 (661)
                      +++.|.|.|+  |..+.        +++|++.|++||+|.+|.|++++.+  ++++|+|||+|.+.++|.+|++.+ +..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4568899998  43443        4699999999999999999988764  468999999999999999999987 689


Q ss_pred             cCCeEEEEEeccCC
Q psy15852        250 INDKEVDVKKATPK  263 (661)
Q Consensus       250 ~~g~~i~V~~a~~k  263 (661)
                      ++||.|.|.++...
T Consensus        84 f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           84 FANRVVVTKYCDPD   97 (105)
T ss_dssp             ETTEECEEEEECHH
T ss_pred             eCCCEEEEEEeCHH
Confidence            99999999998653

>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=99.14  E-value=2e-10  Score=99.84  Aligned_cols=80  Identities=9%  Similarity=0.232  Sum_probs=67.3

Q ss_pred             ccCCeeEecCCCccC-----------CHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCc
Q psy15852        182 AKSGKIFVGGLSPEM-----------KDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQK  249 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~-----------te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~  249 (661)
                      ..+++|+|+||....           ++++|+++|++||.|.+|.| .++   .++|||||+|.+.++|.+|++.+ +..
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            346899999994332           26899999999999999966 443   37999999999999999999887 689


Q ss_pred             cCCeEEEEEeccCCCC
Q psy15852        250 INDKEVDVKKATPKPE  265 (661)
Q Consensus       250 ~~g~~i~V~~a~~k~~  265 (661)
                      ++|++|.|.++.++..
T Consensus        89 ~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           89 FGGRQITAQAWDGTTD  104 (112)
T ss_dssp             ETTEECEEEECCSCCC
T ss_pred             ECCcEEEEEEeCCCCC
Confidence            9999999999988654

>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=99.13  E-value=7.9e-11  Score=100.96  Aligned_cols=67  Identities=19%  Similarity=0.314  Sum_probs=60.4

Q ss_pred             CHHHHHHHhhcCCCeeEEEEeeCCCC--CCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhhc
Q psy15852        112 ITEELKEHFSKYGEIENVTLKSDPNT--GRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKA  182 (661)
Q Consensus       112 te~~L~~~F~~~G~I~~v~l~~~~~t--g~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~~  182 (661)
                      .+++|++.|++||+|.+|+|++++.+  ++++|||||+|.++++|.+|    +..+|+..+.||.|.|.++..
T Consensus        28 ~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~A----i~~lnG~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           28 IVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKA----MQGLTGRKFANRVVVTKYCDP   96 (105)
T ss_dssp             HHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHH----HHHHTTCEETTEECEEEEECH
T ss_pred             HHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHH----HHHhCCCEeCCCEEEEEEeCH
Confidence            45799999999999999999998764  36899999999999999999    999999999999999887643

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

Probab=99.13  E-value=3e-10  Score=96.08  Aligned_cols=66  Identities=9%  Similarity=0.224  Sum_probs=58.6

Q ss_pred             ccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCCCC
Q psy15852        194 PEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE  265 (661)
Q Consensus       194 ~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k~~  265 (661)
                      ..+++++|+++|++||+|.+|.|+     ++++|||||+|.+.++|.+|++.+ ..+.+++|.|.|+.++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~-~~~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNE-VGLVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTC-CBCSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhc-CCCCCCeEEEEEccCCCC
Confidence            568999999999999999999997     357999999999999999999984 446799999999987653

>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=99.12  E-value=7.4e-11  Score=100.99  Aligned_cols=66  Identities=30%  Similarity=0.481  Sum_probs=58.1

Q ss_pred             cCCHHHHHHHh------------hcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852        110 HKITEELKEHF------------SKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus       110 ~~te~~L~~~F------------~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      .+++++|+++|            ++||+|.+|+|++++. ++++|||||+|.++++|.+|    +..+|+..+.|++|.|
T Consensus        26 ~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A----~~~lng~~~~Gr~i~v  100 (104)
T 1jmt_A           26 AVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKA----VIDLNNRWFNGQPIHA  100 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHH----HHHHTTCEETTEECCE
T ss_pred             ccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHH----HHHHCCCEECCEEEEE
Confidence            55666666555            9999999999999865 89999999999999999999    9999999999999988


Q ss_pred             hhh
Q psy15852        178 KKA  180 (661)
Q Consensus       178 ~~~  180 (661)
                      .++
T Consensus       101 ~~s  103 (104)
T 1jmt_A          101 ELS  103 (104)
T ss_dssp             EEC
T ss_pred             EEc
Confidence            754

>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=99.12  E-value=6.8e-11  Score=103.40  Aligned_cols=78  Identities=17%  Similarity=0.253  Sum_probs=65.9

Q ss_pred             CcEEEEcCCC---c---CCHHHHHHHhhcCCCeeEEEEeeCCC----CCCcccEEEEEEeehhhHHHhhHHHHHHhCCee
Q psy15852        100 NKMVSHPGIV---H---KITEELKEHFSKYGEIENVTLKSDPN----TGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV  169 (661)
Q Consensus       100 ~~~~~~~~~~---~---~te~~L~~~F~~~G~I~~v~l~~~~~----tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~  169 (661)
                      .++|+..|..   +   -.+++|++.|++||+|.+|+|++++.    +++++||+||+|.++++|.+|    +..+|+..
T Consensus        20 s~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~A----i~~LnGr~   95 (118)
T 3ue2_A           20 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKA----IQALNGRW   95 (118)
T ss_dssp             CCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHH----HHHHTTCE
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHH----HHHHCCCE
Confidence            4455555553   2   24789999999999999999999864    467899999999999999999    99999999


Q ss_pred             ecceeehhhhhh
Q psy15852        170 INNKKIEAKKAK  181 (661)
Q Consensus       170 i~g~~i~v~~~~  181 (661)
                      +.||.|.+.++.
T Consensus        96 f~GR~i~v~~~~  107 (118)
T 3ue2_A           96 FAGRKVVAEVYD  107 (118)
T ss_dssp             ETTEECEEEEEC
T ss_pred             ECCcEEEEEEcC
Confidence            999999987764

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

Probab=99.12  E-value=2.7e-10  Score=96.40  Aligned_cols=52  Identities=25%  Similarity=0.328  Sum_probs=47.6

Q ss_pred             CCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCccc
Q psy15852        603 VDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY  659 (661)
Q Consensus       603 ~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~~  659 (661)
                      .++|+++|+++|++||.|.+|+|+     ++++|||||+|.+.++|.+|++..+.+.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~~~   78 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVGLV   78 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCBCS
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCCCC
Confidence            468999999999999999999998     5789999999999999999999877654

>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=99.11  E-value=1.3e-10  Score=101.02  Aligned_cols=63  Identities=24%  Similarity=0.402  Sum_probs=57.0

Q ss_pred             HHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhhcc
Q psy15852        113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKAK  183 (661)
Q Consensus       113 e~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~~~  183 (661)
                      +++|+++|++||+|.+|.| .++   .++|||||+|.+.++|++|    +..+|+..+.|++|.|.++.++
T Consensus        40 e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~A----i~~lng~~~~gr~l~v~~a~~~  102 (112)
T 2dit_A           40 REDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYC----IQTLDGRWFGGRQITAQAWDGT  102 (112)
T ss_dssp             HHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHH----HHHSTTCEETTEECEEEECCSC
T ss_pred             HHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHH----HHHcCCCEECCcEEEEEEeCCC
Confidence            6899999999999999966 443   3899999999999999999    9999999999999999998764

>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=99.09  E-value=5.1e-11  Score=101.97  Aligned_cols=71  Identities=14%  Similarity=0.311  Sum_probs=61.2

Q ss_pred             ecCCCccCCHHHHHHHH------------hcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEE
Q psy15852        189 VGGLSPEMKDEEIKAHF------------AQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEV  255 (661)
Q Consensus       189 V~nLp~~~te~~L~~~F------------~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i  255 (661)
                      +.+||..+++++|++.|            ++||+|.+|.|+++.. ++++|||||+|.+.++|.+|++.+ +..++||.|
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 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            45677777777766655            9999999999998765 789999999999999999999986 689999999


Q ss_pred             EEEec
Q psy15852        256 DVKKA  260 (661)
Q Consensus       256 ~V~~a  260 (661)
                      .|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99886

>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=99.06  E-value=1.9e-10  Score=100.49  Aligned_cols=81  Identities=11%  Similarity=0.164  Sum_probs=69.8

Q ss_pred             ccCCeeEecCCCc--cC---CHHHHHHHHhcCCCeEEEEeccCCC----CCCcCcEEEEEeCCHHHHHHHHHhC-CCccC
Q psy15852        182 AKSGKIFVGGLSP--EM---KDEEIKAHFAQFGNIIETEMPYDKS----KSQRKNFCFITFEHESVVIDLLKNP-KQKIN  251 (661)
Q Consensus       182 ~~~~~lfV~nLp~--~~---te~~L~~~F~~~G~i~~v~i~~~~~----~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~  251 (661)
                      +++++|+|+|+-.  ++   .++||++.|++||+|.+|.|++++.    +++++|++||+|.+.++|.+|++.+ +..++
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            4678999999932  22   3689999999999999999998764    4577899999999999999999997 68999


Q ss_pred             CeEEEEEeccC
Q psy15852        252 DKEVDVKKATP  262 (661)
Q Consensus       252 g~~i~V~~a~~  262 (661)
                      ||.|.|.++..
T Consensus        98 GR~i~v~~~~~  108 (118)
T 3ue2_A           98 GRKVVAEVYDQ  108 (118)
T ss_dssp             TEECEEEEECH
T ss_pred             CcEEEEEEcCh
Confidence            99999999865

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.05  E-value=1.7e-10  Score=113.09  Aligned_cols=76  Identities=26%  Similarity=0.335  Sum_probs=64.4

Q ss_pred             CCcEEEEcCCC-cC---------CHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCe
Q psy15852         99 KNKMVSHPGIV-HK---------ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH  168 (661)
Q Consensus        99 ~~~~~~~~~~~-~~---------te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~  168 (661)
                      ..+.|||++++ .+         +|++|+++|++||+|.+|+|+.      +||||||+|.+.++|+.|    +..+++.
T Consensus       133 ~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A----~~am~g~  202 (240)
T 3u1l_A          133 KNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFA----KEAMSNQ  202 (240)
T ss_dssp             CCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHH----HHHHTTC
T ss_pred             CCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHH----HHHhCCC
Confidence            34555556655 76         7999999999999999999985      479999999999999999    9999999


Q ss_pred             ee------------cceeehhhhhhccC
Q psy15852        169 VI------------NNKKIEAKKAKAKS  184 (661)
Q Consensus       169 ~i------------~g~~i~v~~~~~~~  184 (661)
                      .|            .|+.|.|.|+....
T Consensus       203 ~l~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          203 TLLLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCCCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             EEeccccccccccCCCCEEEEEEccCCC
Confidence            99            89999999997654

>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=99.03  E-value=2.7e-10  Score=117.88  Aligned_cols=62  Identities=16%  Similarity=0.161  Sum_probs=55.3

Q ss_pred             ccCCCeEEEcC--CCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        590 VEAKNKMVSHP--GIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       590 ~~~~~~l~v~n--lp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      ..+.++|||+|  |++.+||++|+++|++||+|.+|.|++      +||||||+|.+.++|++||+.++.
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG   78 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNG   78 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCC
Confidence            34568999999  578999999999999999999988864      479999999999999999998875

>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=98.87  E-value=2.7e-09  Score=110.41  Aligned_cols=80  Identities=9%  Similarity=0.134  Sum_probs=65.8

Q ss_pred             hhhhhhccCCeeEecC--CCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCcc--
Q psy15852        176 EAKKAKAKSGKIFVGG--LSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKI--  250 (661)
Q Consensus       176 ~v~~~~~~~~~lfV~n--Lp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~--  250 (661)
                      .|.....+.++|||+|  |+..+++++|+++|++||+|.+|.++.      +||||||+|.+.++|++|++.+ +..+  
T Consensus        10 ~v~~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~   83 (345)
T 3tht_A           10 GIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVD   83 (345)
T ss_dssp             TCCCCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             CceecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCcccc
Confidence            3455566778999999  578999999999999999999998854      4899999999999999999998 4544  


Q ss_pred             -CCe--EEEEEecc
Q psy15852        251 -NDK--EVDVKKAT  261 (661)
Q Consensus       251 -~g~--~i~V~~a~  261 (661)
                       .|+  .|.|.++.
T Consensus        84 ~~g~~~~ly~~~~~   97 (345)
T 3tht_A           84 DLGQKITLYLNFVE   97 (345)
T ss_dssp             TTSCEEECEEEECS
T ss_pred             ccCCceEEEEEEee
Confidence             345  56777764

>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=98.87  E-value=1.3e-09  Score=94.64  Aligned_cols=62  Identities=18%  Similarity=0.226  Sum_probs=55.8

Q ss_pred             CHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhh
Q psy15852        112 ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAK  181 (661)
Q Consensus       112 te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~  181 (661)
                      .+++|++.|++||.|.+|.|.++.    ++||+||+|.+.++|.+|    +..+||..+.|+.|.|.++.
T Consensus        30 l~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~A----i~~lnG~~f~GR~i~v~~~~   91 (114)
T 3s6e_A           30 IKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAA----VNALHGRWFAGKMITAAYVP   91 (114)
T ss_dssp             HHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHH----HHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHH----HHHhCCCEECCEEEEEEEEc
Confidence            356899999999999999997752    599999999999999999    99999999999999987764

>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=98.76  E-value=9.8e-09  Score=88.99  Aligned_cols=76  Identities=5%  Similarity=0.073  Sum_probs=63.4

Q ss_pred             CCeeEecCCCcc----------CCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC
Q psy15852        184 SGKIFVGGLSPE----------MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND  252 (661)
Q Consensus       184 ~~~lfV~nLp~~----------~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g  252 (661)
                      ++.|.++|+-..          -.++||++.|++||.|.+|.|.++.    ++|++||+|.+.++|.+|++.+ +..++|
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            467888887322          2246899999999999999997753    4899999999999999999987 689999


Q ss_pred             eEEEEEeccCC
Q psy15852        253 KEVDVKKATPK  263 (661)
Q Consensus       253 ~~i~V~~a~~k  263 (661)
                      |.|.|.++...
T Consensus        83 R~i~v~~~~~~   93 (114)
T 3s6e_A           83 KMITAAYVPLP   93 (114)
T ss_dssp             EECEEEEECHH
T ss_pred             EEEEEEEEcHH
Confidence            99999998653

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.72  E-value=2.1e-08  Score=87.07  Aligned_cols=59  Identities=19%  Similarity=0.230  Sum_probs=54.5

Q ss_pred             cCCCeEEEcCCCCC-CCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcC-HHHHHHHHHhC
Q psy15852        591 EAKNKMVSHPGIVD-KITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKD-TESLEKASVED  655 (661)
Q Consensus       591 ~~~~~l~v~nlp~~-~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~-~e~A~~A~~~~  655 (661)
                      ..+.-|+|.||+++ +++++|+++|++||.|.+|.+.++..      .|||.|.+ .++|..|+.++
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~l   76 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDA   76 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHT
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHh
Confidence            35788999999999 99999999999999999999999876      69999999 79999999875

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.66  E-value=4.9e-08  Score=84.71  Aligned_cols=74  Identities=15%  Similarity=0.160  Sum_probs=65.2

Q ss_pred             ccCCeeEecCCCcc-CCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCC-HHHHHHHHHhC---CCccCCeEEE
Q psy15852        182 AKSGKIFVGGLSPE-MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH-ESVVIDLLKNP---KQKINDKEVD  256 (661)
Q Consensus       182 ~~~~~lfV~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~-~~~A~~Al~~~---~~~~~g~~i~  256 (661)
                      ++.+-|+|+||+.. +++++|+++|++||+|.+|.+.++..      .|||+|.+ .++|.+|++.+   +..|+|..+.
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            45678999999999 99999999999999999999988754      49999999 88999999986   4689998888


Q ss_pred             EEecc
Q psy15852        257 VKKAT  261 (661)
Q Consensus       257 V~~a~  261 (661)
                      ++...
T Consensus        90 ~evL~   94 (121)
T 1owx_A           90 WEVLE   94 (121)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            87654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.60  E-value=1.6e-07  Score=76.20  Aligned_cols=75  Identities=23%  Similarity=0.427  Sum_probs=62.3

Q ss_pred             ccCCeeEecCCCc----cCCH----HHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCe
Q psy15852        182 AKSGKIFVGGLSP----EMKD----EEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDK  253 (661)
Q Consensus       182 ~~~~~lfV~nLp~----~~te----~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~  253 (661)
                      |+..+|+|.-++.    ++-+    .+|.+.|++||+|..++++.++        +||+|.+.++|.+|++.++..+.||
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~mnG~~v~Gr   76 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLSLNGKELLNR   76 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGGGTTCEETTE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHhcCCeEeCCe
Confidence            4456888877662    2323    5799999999999999998763        8999999999999999668999999


Q ss_pred             EEEEEeccCCC
Q psy15852        254 EVDVKKATPKP  264 (661)
Q Consensus       254 ~i~V~~a~~k~  264 (661)
                      .|+|+.+.+.-
T Consensus        77 ~LkV~lkt~dW   87 (91)
T 2dnr_A           77 TITIALKSPSG   87 (91)
T ss_dssp             EEEEEECCCSS
T ss_pred             EEEEEeCCCCc
Confidence            99999998754

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.47  E-value=2.1e-07  Score=75.51  Aligned_cols=56  Identities=18%  Similarity=0.329  Sum_probs=51.2

Q ss_pred             HHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhhc
Q psy15852        114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKA  182 (661)
Q Consensus       114 ~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~~  182 (661)
                      .+|.+.|++||+|..++++.++        +||+|.+.++|.+|    +. +|+..+.|+.|+|..+.+
T Consensus        30 ~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaA----i~-mnG~~v~Gr~LkV~lkt~   85 (91)
T 2dnr_A           30 DELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNV----LS-LNGKELLNRTITIALKSP   85 (91)
T ss_dssp             HHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHG----GG-GTTCEETTEEEEEEECCC
T ss_pred             HHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHH----Hh-cCCeEeCCeEEEEEeCCC
Confidence            6799999999999999999873        89999999999998    65 999999999999988765

>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=98.38  E-value=2.5e-07  Score=90.58  Aligned_cols=68  Identities=18%  Similarity=0.257  Sum_probs=60.5

Q ss_pred             cCCHHHHHHHhhcCCCeeEEEEeeCCC----CCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhh
Q psy15852        110 HKITEELKEHFSKYGEIENVTLKSDPN----TGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAK  181 (661)
Q Consensus       110 ~~te~~L~~~F~~~G~I~~v~l~~~~~----tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~  181 (661)
                      +-.+++|++.|++||.|.+|.|+++..    +++++|++||+|.+.++|.+|    +..+||..+.||.|.+....
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a----~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKA----IQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHH----HHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHH----HHHhcCceECCeEEEEEEcC
Confidence            456789999999999999999996544    458999999999999999999    99999999999999887654

>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=98.32  E-value=4.9e-07  Score=73.71  Aligned_cols=73  Identities=15%  Similarity=0.300  Sum_probs=61.0

Q ss_pred             ccCCeeEecCCCcc-----CCH----HHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCC
Q psy15852        182 AKSGKIFVGGLSPE-----MKD----EEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKIND  252 (661)
Q Consensus       182 ~~~~~lfV~nLp~~-----~te----~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g  252 (661)
                      |+..+|+|.-++..     +-+    .+|.+.|++||+|..+++..++        +||+|.+.++|.+||+..+..++|
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG~~v~G   84 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMKVKG   84 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGGSEETT
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHhcCCeeeCC
Confidence            55679999887632     222    4689999999999999998764        999999999999999966899999


Q ss_pred             eEEEEEeccC
Q psy15852        253 KEVDVKKATP  262 (661)
Q Consensus       253 ~~i~V~~a~~  262 (661)
                      |.|+|++..+
T Consensus        85 r~L~V~~k~~   94 (95)
T 1ufw_A           85 RAVKISGPSS   94 (95)
T ss_dssp             EEEEEECCCC
T ss_pred             eEEEEeccCC
Confidence            9999987653

>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=98.21  E-value=1.7e-06  Score=84.51  Aligned_cols=68  Identities=12%  Similarity=0.142  Sum_probs=59.7

Q ss_pred             cCCHHHHHHHHhcCCCeEEEEeccCC----CCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        195 EMKDEEIKAHFAQFGNIIETEMPYDK----SKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       195 ~~te~~L~~~F~~~G~i~~v~i~~~~----~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      .-.+++|++.|++||.|.++.|+++.    .+++++|++||+|.+.++|.+|++.+ +..+.||.|.+.+...
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            34568999999999999999998543    44589999999999999999999997 6899999999999764

>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=98.21  E-value=7.4e-07  Score=72.69  Aligned_cols=55  Identities=16%  Similarity=0.301  Sum_probs=49.8

Q ss_pred             HHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhh
Q psy15852        114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAK  181 (661)
Q Consensus       114 ~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~  181 (661)
                      .+|.+.|++||.|..|+++.++        +||+|.+.++|.+|    +. +++..+.|+.|+|....
T Consensus        39 ~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~A----I~-ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           39 TELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSV----LD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHH----HH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHH----Hh-cCCeeeCCeEEEEeccC
Confidence            5699999999999999999873        99999999999998    65 99999999999987653

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.65  E-value=0.00014  Score=60.47  Aligned_cols=69  Identities=19%  Similarity=0.198  Sum_probs=59.7

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcC-----CCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeeccee
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKY-----GEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK  174 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~-----G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~  174 (661)
                      +++-+-+++..+++..|+.+.+++     |.|..|.+..|..      =|+|+|.+...|-+|    .+.++|..|.|++
T Consensus        22 rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~------GAivef~d~~~AgKa----sLaL~G~ef~gr~   91 (117)
T 2l9w_A           22 TLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN------GAIIIFRDSKFAAKM----LMILNGSQFQGKV   91 (117)
T ss_dssp             SCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT------EEEEECSCHHHHHHH----HHHHSSEEETTEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC------ceEEEEccchhhHHH----HhhcCCeeecCeE
Confidence            444444555589999999999999     9999999998854      599999999999999    9999999999999


Q ss_pred             ehhh
Q psy15852        175 IEAK  178 (661)
Q Consensus       175 i~v~  178 (661)
                      |.+.
T Consensus        92 Lr~g   95 (117)
T 2l9w_A           92 IRSG   95 (117)
T ss_dssp             EEEE
T ss_pred             EEec
Confidence            8764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.52  E-value=0.00028  Score=58.24  Aligned_cols=86  Identities=15%  Similarity=0.231  Sum_probs=71.5

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcC-----CCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecce
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKY-----GEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK  173 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~-----G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~  173 (661)
                      ..++.+.++++++.++.|.-+|+.-     |+|.+|....        +-|+|+|.+.+.|++     +++...+.|.+.
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~r-----VL~k~~H~L~~~   74 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAER-----VLAQADHELHGA   74 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHH-----HHTCSCCBSSSS
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHH-----HhcCCcceecCe
Confidence            4566677777799999999999872     5799998865        269999999999999     788889999999


Q ss_pred             eehhhhhhcc-CCeeEecCCCccCC
Q psy15852        174 KIEAKKAKAK-SGKIFVGGLSPEMK  197 (661)
Q Consensus       174 ~i~v~~~~~~-~~~lfV~nLp~~~t  197 (661)
                      ++.|.+..+. ..+|++.+|++.++
T Consensus        75 ~LsV~P~~~~~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           75 QLSLRPAPPRAPARLLLQGLPPGTS   99 (104)
T ss_dssp             BCEEEECCCCCCCCCCCCSCCCCCC
T ss_pred             EEEEEcCCCCCcceEeeecCCCCCC
Confidence            9999876554 47999999998875

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.46  E-value=0.00076  Score=55.66  Aligned_cols=74  Identities=18%  Similarity=0.271  Sum_probs=64.4

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhc-----CCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEE
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQ-----FGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVK  258 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~-----~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~  258 (661)
                      .++|.|.|||+.+.++.|+-+|++     =|+|.+++...        +-|+|+|.+.+.|++.|+...+.|++.+|.|.
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV~   79 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLSLR   79 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEEEE
Confidence            368999999999999999999987     25899988753        45999999999999999998999999999999


Q ss_pred             eccCCCC
Q psy15852        259 KATPKPE  265 (661)
Q Consensus       259 ~a~~k~~  265 (661)
                      ...++..
T Consensus        80 P~~~~~~   86 (104)
T 2dhx_A           80 PAPPRAP   86 (104)
T ss_dssp             ECCCCCC
T ss_pred             cCCCCCc
Confidence            8777653

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.43  E-value=0.00031  Score=58.41  Aligned_cols=71  Identities=15%  Similarity=0.090  Sum_probs=62.5

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcC-----CCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHh-CCCccCCeEEEE
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQF-----GNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN-PKQKINDKEVDV  257 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~-----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~-~~~~~~g~~i~V  257 (661)
                      .++|-+-|||..+++..|+.+..++     |.|..+.+..|.      +-|+|+|.+...|-||.-. .+..|.|++|++
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~   94 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRS   94 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEEe
Confidence            5789999999999999999999999     999999998763      4599999999999998755 478999999999


Q ss_pred             Eec
Q psy15852        258 KKA  260 (661)
Q Consensus       258 ~~a  260 (661)
                      .-.
T Consensus        95 gTv   97 (117)
T 2l9w_A           95 GTI   97 (117)
T ss_dssp             ECH
T ss_pred             cCH
Confidence            653

>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=96.40  E-value=0.0043  Score=50.49  Aligned_cols=52  Identities=21%  Similarity=0.296  Sum_probs=44.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        595 KMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       595 ~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      .||+-..|.+|--.||.++|++||.| .|+=+-|-       -|||.|.+++.|..|++.
T Consensus        17 HVf~l~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~   68 (100)
T 1whv_A           17 HVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHH
T ss_pred             eEEEEeCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHh
Confidence            35555999999999999999999976 66777654       599999999999999984

>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=96.27  E-value=0.021  Score=48.64  Aligned_cols=73  Identities=21%  Similarity=0.284  Sum_probs=60.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCC-eEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKIND-KEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g-~~i~V~~a~  261 (661)
                      ..+.|.|-+.|+.. ...|...|++||.|.+....      ....+-.|+|.++.+|++||.+++..+.+ -.|-|.+..
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEECC
Confidence            34678898999986 45677899999999988872      23678999999999999999999988874 778888865


Q ss_pred             C
Q psy15852        262 P  262 (661)
Q Consensus       262 ~  262 (661)
                      .
T Consensus        96 d   96 (119)
T 1wwh_A           96 D   96 (119)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=96.21  E-value=0.0054  Score=50.12  Aligned_cols=51  Identities=22%  Similarity=0.294  Sum_probs=43.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        596 MVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       596 l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      ||+-..|.+|--.||.++|++||.| .|+=+-|-       -|||.|.+++.|..|++.
T Consensus         8 V~~l~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~   58 (101)
T 3ctr_A            8 VLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAVNT   58 (101)
T ss_dssp             EEEEECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHHHH
T ss_pred             EEEEeCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHh
Confidence            4555999999999999999999955 66666654       599999999999999984

>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=96.08  E-value=0.011  Score=48.91  Aligned_cols=61  Identities=11%  Similarity=0.043  Sum_probs=51.5

Q ss_pred             CCCeEEEcCCCCCC-C----HHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        592 AKNKMVSHPGIVDK-I----TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       592 ~~~~l~v~nlp~~~-t----e~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ..++|+|.||+.++ +    .+.++++|..|+++.+....+.-.      =..|.|.++++|.+|-.++|.+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR------Rirv~F~~~~~A~~AR~~Lh~~   69 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNPLSAADARLRLHKT   69 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT------EEEEECSSTTHHHHHHHTSTTS
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce------EEEEEeCChHHHHHHHHHhccc
Confidence            46899999998844 2    357899999999999999987654      4689999999999999998864

>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=95.86  E-value=0.015  Score=47.37  Aligned_cols=52  Identities=21%  Similarity=0.331  Sum_probs=44.2

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA  157 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A  157 (661)
                      ....+|++.-|+++...||.++|+.||-| .|+++-|-       .|||.|.+++.|..|
T Consensus        14 ~r~HVf~l~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~a   65 (100)
T 1whv_A           14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIA   65 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHH
T ss_pred             CCCeEEEEeCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHH
Confidence            34568888777799999999999999965 67788763       699999999999997

>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=95.78  E-value=0.029  Score=45.60  Aligned_cols=61  Identities=21%  Similarity=0.164  Sum_probs=48.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCC--cccEEEEEEcCHHHHHHHHHh
Q psy15852        594 NKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGR--SRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       594 ~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~--s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      +||.||+||+..||+++.+..+++..+....-+..+.+..  .-.-|+|.|.+.+++..-.+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~   64 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDR   64 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHH
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHH
Confidence            5899999999999999999999999887777665433211  224699999999888877664

>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=95.73  E-value=0.043  Score=44.62  Aligned_cols=70  Identities=20%  Similarity=0.118  Sum_probs=54.9

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCC--cccEEEEEEeehhhHHHhhHHHHHHhCCeeecce
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGR--SRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK  173 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~--srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~  173 (661)
                      .|+++..|||.+||+++.+.++.+..+.....+..+.+..  .-.-|||.|.+.+++..-    ....+|+.+.+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f----~~~~~g~~F~D~   73 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILF----RDRFDGYVFLDN   73 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHH----HHHHTTCEEECT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHH----HHHhCCcEEEcC
Confidence            4788999999999999999999998877666665443222  223599999999999986    778898887543

>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=95.56  E-value=0.027  Score=46.61  Aligned_cols=72  Identities=11%  Similarity=0.051  Sum_probs=56.7

Q ss_pred             CcEEEEcCCCcC-----CHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeeccee
Q psy15852        100 NKMVSHPGIVHK-----ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK  174 (661)
Q Consensus       100 ~~~~~~~~~~~~-----te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~  174 (661)
                      +++++.++.+++     -.+.++++|..|+++.+....+.-.      =..|.|.++++|.+|    -..+++..+.|+.
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR------Rirv~F~~~~~A~~A----R~~Lh~~~f~g~~   75 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNPLSAADA----RLRLHKTEFLGKE   75 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT------EEEEECSSTTHHHHH----HHTSTTSEETTEE
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce------EEEEEeCChHHHHHH----HHHhccceecCce
Confidence            456666665433     2367899999999988887776432      478999999999999    8999999999998


Q ss_pred             ehhhhhh
Q psy15852        175 IEAKKAK  181 (661)
Q Consensus       175 i~v~~~~  181 (661)
                      +++-.+.
T Consensus        76 ~r~YFgq   82 (104)
T 1wey_A           76 MKLYFAQ   82 (104)
T ss_dssp             CEEECCC
T ss_pred             eEEEecC
Confidence            8775554

>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=95.27  E-value=0.046  Score=44.67  Aligned_cols=50  Identities=22%  Similarity=0.325  Sum_probs=42.5

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA  157 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A  157 (661)
                      ..+|+++-|+++...||.++|+.||-| .|+++-|-       .|||.|.+++.|..|
T Consensus         6 ~HV~~l~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~a   55 (101)
T 3ctr_A            6 DHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIA   55 (101)
T ss_dssp             EEEEEEECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHH
T ss_pred             CeEEEEeCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHH
Confidence            346778777799999999999999944 78888763       699999999999997

>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=95.13  E-value=0.068  Score=45.55  Aligned_cols=62  Identities=15%  Similarity=0.304  Sum_probs=47.9

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecc
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN  172 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g  172 (661)
                      .+-|.|-..|.-....|...|++||.|.+......      ...-.|.|.++.+|++|     +..|+..|.+
T Consensus        24 ~~wVtVFGFp~~~~~~VL~~F~~~G~Iv~~~~~~~------~NWihI~Y~s~~~A~rA-----L~kNG~ii~g   85 (119)
T 1wwh_A           24 DTWVTVFGFPQASASYILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKA-----LSKDGRIFGE   85 (119)
T ss_dssp             GGEEEEECCCGGGHHHHHHHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHH-----HTTTTCEETT
T ss_pred             CCEEEEECCCHHHHHHHHHHHHhhCcEEEeccCCC------CCeEEEEeCCHHHHHHH-----HHhCCeEecC
Confidence            33444445554468889999999999998887332      23899999999999995     7789999875

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.25  E-value=0.061  Score=46.46  Aligned_cols=77  Identities=23%  Similarity=0.322  Sum_probs=56.4

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEE-EEeccCC--------CCC-----CcCcEEEEEeCCHHHHHHHHHhCCCcc
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIE-TEMPYDK--------SKS-----QRKNFCFITFEHESVVIDLLKNPKQKI  250 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~-v~i~~~~--------~~g-----~~~g~afV~f~~~~~A~~Al~~~~~~~  250 (661)
                      ..|.|-+.|+.... .+-+.|++||.|.+ ....+..        ...     .......|+|+++.+|.+||..++..+
T Consensus         8 ~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~ii   86 (132)
T 3p3d_A            8 LAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAVF   86 (132)
T ss_dssp             CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCEE
T ss_pred             eEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeEe
Confidence            45777788877665 56678999999866 2222100        000     125677999999999999999999999


Q ss_pred             CCeEEEEEeccC
Q psy15852        251 NDKEVDVKKATP  262 (661)
Q Consensus       251 ~g~~i~V~~a~~  262 (661)
                      .|.-|-|.+..+
T Consensus        87 ~G~mIGV~Py~~   98 (132)
T 3p3d_A           87 NGVLLGVIPYTK   98 (132)
T ss_dssp             TTEECEEEECCH
T ss_pred             CcEEEEEEECCH
Confidence            999999988754

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=93.97  E-value=0.068  Score=43.73  Aligned_cols=70  Identities=10%  Similarity=0.002  Sum_probs=48.2

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCC--cccEEEEEEeehhhHHHhhHHHHHHhCCeeecc
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGR--SRGFAFIVFKDTESLEKASVEDVIAEGNHVINN  172 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~--srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g  172 (661)
                      ..++++..|||.+||+++.+.++.+=++.....+..+.+..  .-.-|||.|.+.++...-    ....++..+.+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F----~~~f~g~~F~D   80 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLF----RDRFDGYIFLD   80 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHH----HHHSTTEEEEC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHH----HHHcCCcEEEe
Confidence            46899999999999999888877654442222222111111  112489999999999986    77888887754

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.43  E-value=0.047  Score=58.22  Aligned_cols=56  Identities=11%  Similarity=0.191  Sum_probs=42.8

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHh
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN  245 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~  245 (661)
                      .+.|+|. .|..+++.+|.++|++||+|.++.+-.+.     .-||.|+|.+.+++.+++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhc
Confidence            3789997 79999999999999999999999886542     46999999999999988765

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=91.84  E-value=0.29  Score=40.01  Aligned_cols=63  Identities=11%  Similarity=0.118  Sum_probs=44.2

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCc--CcEEEEEeCCHHHHHHHHHhC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQR--KNFCFITFEHESVVIDLLKNP  246 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~--~g~afV~f~~~~~A~~Al~~~  246 (661)
                      +-+|-|+.||+.+||+++.+.++..=++....+...+.+.+.  -.-|||.|.+.++...-.+..
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f   73 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRF   73 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHS
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHc
Confidence            357999999999999999988887655544333332222111  123899999999988877764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=91.25  E-value=0.091  Score=56.01  Aligned_cols=57  Identities=19%  Similarity=0.243  Sum_probs=43.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      ..+.|||. .|.+.++++|.+.|++||.|.++.+-.+.  |   =||.|+|.+.++|.+++..
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC---CCHHHHSS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHHHHHHHHhc
Confidence            35679997 89999999999999999999998877543  3   4999999999999988764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=90.62  E-value=0.17  Score=43.70  Aligned_cols=75  Identities=15%  Similarity=0.255  Sum_probs=50.6

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeE-EEEeeCC--------CCC-----CcccEEEEEEeehhhHHHhhHHHHHHh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIEN-VTLKSDP--------NTG-----RSRGFAFIVFKDTESLEKASVEDVIAE  165 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~-v~l~~~~--------~tg-----~srG~afV~F~~~e~A~~A~~~~~~~~  165 (661)
                      ..-|+|=..|......+.+.|++||.|.+ +.+.+..        ...     .....-.|+|.++.+|.+|     +..
T Consensus         7 e~~VtVFGFp~~~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rA-----L~~   81 (132)
T 3p3d_A            7 ELAILVFGYPETMANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDA-----LLE   81 (132)
T ss_dssp             -CEEEEECCCGGGHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHH-----HTT
T ss_pred             ceEEEEEecCHHHHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHH-----HHh
Confidence            34455555577778889999999999866 3222100        000     1245779999999999995     788


Q ss_pred             CCeeecceeehhhh
Q psy15852        166 GNHVINNKKIEAKK  179 (661)
Q Consensus       166 ~~~~i~g~~i~v~~  179 (661)
                      ||..|.|.-|-|.+
T Consensus        82 NG~ii~G~mIGV~P   95 (132)
T 3p3d_A           82 NGAVFNGVLLGVIP   95 (132)
T ss_dssp             TTCEETTEECEEEE
T ss_pred             CCeEeCcEEEEEEE
Confidence            99999986444433

---

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	661
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-22
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-04
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	6e-17
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-10
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-06
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	9e-17
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-04
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-15
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-04
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	4e-15
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-04
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-04
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-14
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	5e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-07
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	5e-14
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	9e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-05
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	0.002
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-13
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-09
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	8e-13
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	9e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	9e-13
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-06
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-12
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-10
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	7e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-12
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-12
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-05
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	0.002
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	0.003
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-05
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-04
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	8e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	7e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	6e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-11
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-04
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-07
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-04
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-07
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	0.002
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-11
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-08
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-04
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-11
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	0.004
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-11
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-08
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	5e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-10
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-04
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-04
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-10
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-06
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	7e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	9e-04
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	8e-10
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	0.001
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	9e-10
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-07
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	0.001
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	0.001
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-05
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-05
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-04
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-09
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-09
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	5e-04
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-09
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	0.001
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	6e-09
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	3e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-09
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	7e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-08
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-08
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	0.002
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-08
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-08
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	8e-05
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	0.002
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-04
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	4e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	0.002
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	4e-08
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	0.002
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	0.002
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-08
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-08
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	7e-08
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	3e-04
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-07
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-04
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	0.002
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	0.001
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	0.002
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	5e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	9e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-06
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	9e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-04
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	4e-04
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.001
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:) 0.002
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:) 0.002
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:) 0.003
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	0.002
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	0.002
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	0.003
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	0.004

>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 = 92.4 bits (228), Expect = 3e-22
 Identities = 43/158 (27%), Positives = 78/158 (49%), Gaps = 6/158 (3%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           E L+ HF ++G + +  +  DPNT RSRGF F+ +   E ++ A           V+  K
Sbjct: 21  ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPK 80

Query: 174 KIEAKK------AKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKN 227
           +  +++      A     KIFVGG+  + ++  ++ +F Q+G I   E+  D+   +++ 
Sbjct: 81  RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG 140

Query: 228 FCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           F F+TF+    V  ++      +N    +V+KA  K E
Sbjct: 141 FAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE 178

>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 = 57.3 bits (137), Expect = 4e-10
 Identities = 31/170 (18%), Positives = 66/170 (38%), Gaps = 11/170 (6%)

Query: 20  GGAPVSVKDDD-RKLFCPLSSYLELDYLQLWQ---YFDWVSSSFSENCLLEDSIGKPLTV 75
           GG      D+  R  F    +  +   ++         +   +++    ++ ++      
Sbjct: 12  GGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK 71

Query: 76  SCSHHYYLFDQILRTHFFYIMEAKNKMVSHPGIVHKIT--EELKEHFSKYGEIENVTLKS 133
                      + R                 G + + T    L+++F +YG+IE + + +
Sbjct: 72  VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMT 131

Query: 134 DPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKAK 183
           D  +G+ RGFAF+ F D +S++K      + +  H +N    E +KA +K
Sbjct: 132 DRGSGKKRGFAFVTFDDHDSVDKI-----VIQKYHTVNGHNCEVRKALSK 176

>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 = 50.4 bits (119), Expect = 1e-07
 Identities = 22/82 (26%), Positives = 44/82 (53%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+F+GGLS E  DE +++HF Q+G + +  +  D +  + + F F+T+     V   +  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 246 PKQKINDKEVDVKKATPKPEPF 267
              K++ + V+ K+A  + +  
Sbjct: 68  RPHKVDGRVVEPKRAVSREDSQ 89

>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 = 44.2 bits (103), Expect = 1e-05
 Identities = 16/74 (21%), Positives = 32/74 (43%)

Query: 426 LVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKIN 485
           +   T+  H+        +I   E+  D+   +++ F F+TF+    V  ++      +N
Sbjct: 105 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVN 164

Query: 486 DKEVDVKKATPKPE 499
               +V+KA  K E
Sbjct: 165 GHNCEVRKALSKQE 178

>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 = 43.5 bits (101), Expect = 2e-05
 Identities = 17/44 (38%), Positives = 27/44 (61%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E L+ HF ++G + +  +  DPNT RSRGF F+ +   E ++ A
Sbjct: 21  ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

>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 = 40.4 bits (93), Expect = 2e-04
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 571 CSHYHYLFDQNLRTHYFYIVEAKNKMVSHPGIVDKITEE-LKEHFSKYGEIENVTLKSDP 629
                     +             K +   GI +   E  L+++F +YG+IE + + +D 
Sbjct: 74  GRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR 133

Query: 630 NTGRSRGFAFIVFKDTESLEKA 651
            +G+ RGFAF+ F D +S++K 
Sbjct: 134 GSGKKRGFAFVTFDDHDSVDKI 155

>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 = 74.2 bits (182), Expect = 6e-17
 Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 1/89 (1%)

Query: 178 KKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
           K+A  K+  + V GL  +  ++++K +F+ FG ++  ++  D      K F F+ F    
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 61

Query: 238 VVIDLLKNPKQKINDKEVDVKKATPKPEP 266
             + ++   +  I+ +  D K    K   
Sbjct: 62  TQVKVMSQ-RHMIDGRWCDCKLPNSKQSQ 89

>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 = 56.5 bits (136), Expect = 1e-10
 Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 7/81 (8%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  K TE+ LKE+FS +GE+  V +K D  TG S+GF F+ F + E+  K         
Sbjct: 15  GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV------MS 68

Query: 166 GNHVINNKKIEAKKAKAKSGK 186
             H+I+ +  + K   +K  +
Sbjct: 69  QRHMIDGRWCDCKLPNSKQSQ 89

>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 = 43.0 bits (101), Expect = 5e-06
 Identities = 19/44 (43%), Positives = 29/44 (65%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ++LKE+FS +GE+  V +K D  TG S+GF F+ F + E+  K 
Sbjct: 23  QDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 66

>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 = 41.9 bits (98), Expect = 1e-05
 Identities = 10/58 (17%), Positives = 21/58 (36%), Gaps = 1/58 (1%)

Query: 443 MEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEP 500
            E++  ++  D      K F F+ F      + ++   +  I+ +  D K    K   
Sbjct: 33  GEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMIDGRWCDCKLPNSKQSQ 89

>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 = 73.1 bits (179), Expect = 9e-17
 Identities = 28/75 (37%), Positives = 46/75 (61%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           KIFVGGLSP+  +E+I+ +F  FG +   E+P D   ++R+ FCFITF+ E  V  +++ 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 246 PKQKINDKEVDVKKA 260
               +   + ++K 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 = 58.4 bits (141), Expect = 1e-11
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+     EE ++E+F  +GE+E++ L  D  T + RGF FI FK+ E ++K      + +
Sbjct: 6   GLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-----MEK 60

Query: 166 GNHVINNKKIEAKKA 180
             H +   K E K 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 = 44.2 bits (104), Expect = 2e-06
 Identities = 18/44 (40%), Positives = 30/44 (68%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E+++E+F  +GE+E++ L  D  T + RGF FI FK+ E ++K 
Sbjct: 14  EKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI 57

>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 = 38.8 bits (90), Expect = 1e-04
 Identities = 15/51 (29%), Positives = 28/51 (54%)

Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
           E+   E+P D   ++R+ FCFITF+ E  V  +++     +   + ++K A
Sbjct: 25  EVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA 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 = 68.5 bits (167), Expect = 3e-15
 Identities = 21/75 (28%), Positives = 44/75 (58%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+F+GGLS +   +++K +F++FG +++  +  D    + + F F+ F+    V  ++  
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 246 PKQKINDKEVDVKKA 260
            + K+N K +D K+A
Sbjct: 61  KEHKLNGKVIDPKRA 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 = 56.9 bits (137), Expect = 4e-11
 Identities = 33/75 (44%), Positives = 52/75 (69%), Gaps = 6/75 (8%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+    T++ LK++FSK+GE+ + TLK DP TGRSRGF F++FK++ES++K      + +
Sbjct: 6   GLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV-----MDQ 60

Query: 166 GNHVINNKKIEAKKA 180
             H +N K I+ K+A
Sbjct: 61  KEHKLNGKVIDPKRA 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 = 43.8 bits (103), Expect = 2e-06
 Identities = 25/44 (56%), Positives = 38/44 (86%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ++LK++FSK+GE+ + TLK DP TGRSRGF F++FK++ES++K 
Sbjct: 14  KDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV 57

>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 = 38.4 bits (89), Expect = 2e-04
 Identities = 12/52 (23%), Positives = 26/52 (50%)

Query: 443 MEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
            E+++  +  D    + + F F+ F+    V  ++   + K+N K +D K+A
Sbjct: 24  GEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA 75

>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 = 69.3 bits (169), Expect = 4e-15
 Identities = 23/90 (25%), Positives = 47/90 (52%)

Query: 176 EAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
             K+ K +  K+F+GGLS E  +E ++ ++ Q+G + +  +  D +  + + F F+TF  
Sbjct: 12  RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 71

Query: 236 ESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
            + V   +      I+ + V+ K+A  + E
Sbjct: 72  MAEVDAAMAARPHSIDGRVVEPKRAVAREE 101

>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 = 53.1 bits (127), Expect = 2e-09
 Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 6/78 (7%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + TEE L+ ++ ++G++ +  +  DP + RSRGF F+ F     ++ A     +A 
Sbjct: 27  GLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA-----MAA 81

Query: 166 GNHVINNKKIEAKKAKAK 183
             H I+ + +E K+A A+
Sbjct: 82  RPHSIDGRVVEPKRAVAR 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 = 38.9 bits (90), Expect = 2e-04
 Identities = 13/44 (29%), Positives = 26/44 (59%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E L+ ++ ++G++ +  +  DP + RSRGF F+ F     ++ A
Sbjct: 35  ESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 78

>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 = 38.9 bits (90), Expect = 2e-04
 Identities = 11/50 (22%), Positives = 23/50 (46%)

Query: 450 MPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 499
           +  D +  + + F F+TF   + V   +      I+ + V+ K+A  + E
Sbjct: 52  VMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREE 101

>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 = 65.8 bits (160), Expect = 3e-14
 Identities = 23/75 (30%), Positives = 42/75 (56%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+F+GGLS +   E ++ +F QFG + E  +  D    + + F F+TF  ++ V  +L  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 246 PKQKINDKEVDVKKA 260
            + +++ K +D K 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 = 59.6 bits (144), Expect = 5e-12
 Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 6/75 (8%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + T+E L+E+F ++GE++   +  DP T RSRGF F+ F D   ++K      +A+
Sbjct: 7   GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-----LAQ 61

Query: 166 GNHVINNKKIEAKKA 180
             H +++K I+ K 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 = 46.5 bits (110), Expect = 2e-07
 Identities = 18/44 (40%), Positives = 28/44 (63%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E L+E+F ++GE++   +  DP T RSRGF F+ F D   ++K 
Sbjct: 15  EGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58

>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 = 65.4 bits (159), Expect = 5e-14
 Identities = 22/75 (29%), Positives = 42/75 (56%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           K+F+GGLS E  DE +++HF Q+G + +  +  D +  + + F F+T+     V   +  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 246 PKQKINDKEVDVKKA 260
              K++ + V+ K+A
Sbjct: 68  RPHKVDGRVVEPKRA 82

>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 = 53.5 bits (128), Expect = 9e-10
 Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 6/77 (7%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  + T+E L+ HF ++G + +  +  DPNT RSRGF F+ +   E ++ A     +  
Sbjct: 13  GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA-----MNA 67

Query: 166 GNHVINNKKIEAKKAKA 182
             H ++ + +E K+A +
Sbjct: 68  RPHKVDGRVVEPKRAVS 84

>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 = 41.6 bits (97), Expect = 2e-05
 Identities = 17/44 (38%), Positives = 27/44 (61%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E L+ HF ++G + +  +  DPNT RSRGF F+ +   E ++ A
Sbjct: 21  ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

>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 = 35.4 bits (81), Expect = 0.002
 Identities = 9/49 (18%), Positives = 22/49 (44%)

Query: 446 IETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
            +  +  D +  + + F F+T+     V   +     K++ + V+ K+A
Sbjct: 34  TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA 82

>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 = 64.3 bits (156), Expect = 2e-13
 Identities = 10/96 (10%), Positives = 36/96 (37%)

Query: 170 INNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFC 229
           +          +  +  +F   L+  ++  +++  F+  G + +  +  D++  + K   
Sbjct: 4   VREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIA 63

Query: 230 FITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 265
           ++ F     V   +    Q++    + V+ +  +  
Sbjct: 64  YVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKN 99

>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 = 53.9 bits (129), Expect = 1e-09
 Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 6/82 (7%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +  +I    L++ FS  G++ +V + SD N+ RS+G A++ F + +     SV   I  
Sbjct: 25  QLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ-----SVPLAIGL 79

Query: 166 GNHVINNKKIEAKKAKAKSGKI 187
               +    I  + ++A+  ++
Sbjct: 80  TGQRLLGVPIIVQASQAEKNRL 101

>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 = 41.2 bits (96), Expect = 3e-05
 Identities = 14/43 (32%), Positives = 28/43 (65%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
            +L++ FS  G++ +V + SD N+ RS+G A++ F + +S+  
Sbjct: 33  RDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 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 = 62.1 bits (150), Expect = 8e-13
 Identities = 30/75 (40%), Positives = 48/75 (64%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           KIFVGGLS     E++K +F QFG + +  + +DK+ ++ + F F+TFE E +V  + + 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 246 PKQKINDKEVDVKKA 260
              +IN+K V+ KKA
Sbjct: 61  HFHEINNKMVECKKA 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 = 44.7 bits (105), Expect = 9e-07
 Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+    T E +K +F ++G++++  L  D  T R RGF F+ F+  + +EK         
Sbjct: 6   GLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV-----CEI 60

Query: 166 GNHVINNKKIEAKKA 180
             H INNK +E KKA
Sbjct: 61  HFHEINNKMVECKKA 75

>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 = 62.4 bits (151), Expect = 9e-13
 Identities = 23/90 (25%), Positives = 42/90 (46%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           KIFVGGL     D  ++ +F  FG+I E  +  D+   + + + F+T    +      K+
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 246 PKQKINDKEVDVKKATPKPEPFGVRGGRGG 275
           P   I+ ++ +V  A    +P  ++ G   
Sbjct: 72  PNPIIDGRKANVNLAYLGAKPRSLQTGFAI 101

>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 = 45.1 bits (106), Expect = 1e-06
 Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 6/79 (7%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+ +  T+  L+++F  +G+IE   + +D  TG+SRG+ F+   D  + E+A       +
Sbjct: 17  GLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA-----CKD 71

Query: 166 GNHVINNKKIEAKKAKAKS 184
            N +I+ +K     A   +
Sbjct: 72  PNPIIDGRKANVNLAYLGA 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 = 62.3 bits (151), Expect = 1e-12
 Identities = 15/89 (16%), Positives = 34/89 (38%), Gaps = 5/89 (5%)

Query: 181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKN-FCFITFEHESVV 239
           K  + KI V  +  +    EI+  F+ FG +    +P   + +     F F+ F  +   
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 240 ---IDLLKNPKQKINDKEVDVKKATPKPE 265
               + L +    +  + + ++ A  +  
Sbjct: 65  KKAFNALCH-STHLYGRRLVLEWADSEVT 92

>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 = 54.2 bits (130), Expect = 6e-10
 Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 5/80 (6%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPN-TGRSRGFAFIVFKDTESLEKASVEDVIA 164
            I  +  +  ++E FS +GE++ V L      TG  RGF F+ F   +  +KA    +  
Sbjct: 15  NIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA-FNAL-- 71

Query: 165 EGNHVINNKKIEAKKAKAKS 184
             +  +  +++  + A ++ 
Sbjct: 72  CHSTHLYGRRLVLEWADSEV 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 = 48.4 bits (115), Expect = 7e-08
 Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 1/45 (2%)

Query: 608 EELKEHFSKYGEIENVTLKSDPN-TGRSRGFAFIVFKDTESLEKA 651
            E++E FS +GE++ V L      TG  RGF F+ F   +  +KA
Sbjct: 23  REIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 67

>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 = 61.3 bits (148), Expect = 1e-12
 Identities = 21/75 (28%), Positives = 41/75 (54%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           KIFVGG+  + ++  ++ +F Q+G I   E+  D+   +++ F F+TF+    V  ++  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 63

Query: 246 PKQKINDKEVDVKKA 260
               +N    +V+KA
Sbjct: 64  KYHTVNGHNCEVRKA 78

>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 = 44.3 bits (104), Expect = 1e-06
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 6/75 (8%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           GI     E  L+++F +YG+IE + + +D  +G+ RGFAF+ F D +S++K      + +
Sbjct: 9   GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI-----VIQ 63

Query: 166 GNHVINNKKIEAKKA 180
             H +N    E +KA
Sbjct: 64  KYHTVNGHNCEVRKA 78

>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 = 62.0 bits (150), Expect = 1e-12
 Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 5/86 (5%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIET--EMPYDKSKSQRKNFCFITFEHESVV---I 240
           ++F+GG+    K EEI    A+    +           K + + F F+ +E         
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 241 DLLKNPKQKINDKEVDVKKATPKPEP 266
             L   + ++   ++ V  A P+ + 
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDV 88

>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 = 42.0 bits (98), Expect = 2e-05
 Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 5/81 (6%)

Query: 107 GIVHKITEE-LKEHFSKYGEIEN--VTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVI 163
           GI      E + E  +K  E     +   S  +  ++RGFAF+ ++   +   A     +
Sbjct: 8   GIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR--RKL 65

Query: 164 AEGNHVINNKKIEAKKAKAKS 184
             G   +   +I    A+ + 
Sbjct: 66  MPGRIQLWGHQIAVDWAEPEI 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 = 36.2 bits (83), Expect = 0.002
 Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 2/46 (4%)

Query: 608 EELKEHFSKYGEIEN--VTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           EE+ E  +K  E     +   S  +  ++RGFAF+ ++   +   A
Sbjct: 16  EEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

>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 = 35.4 bits (81), Expect = 0.003
 Identities = 8/54 (14%), Positives = 19/54 (35%), Gaps = 3/54 (5%)

Query: 450 MPYDKSKSQRKNFCFITFEHESVV---IDLLKNPKQKINDKEVDVKKATPKPEP 500
                 K + + F F+ +E           L   + ++   ++ V  A P+ + 
Sbjct: 35  YASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDV 88

>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 = 61.5 bits (149), Expect = 2e-12
 Identities = 21/90 (23%), Positives = 41/90 (45%), Gaps = 1/90 (1%)

Query: 178 KKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
           +K   KS  ++VG LS    +E+I   F++ G+I +  M  DK K     FCF+ +   +
Sbjct: 1   EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA 60

Query: 238 VVIDLLKNP-KQKINDKEVDVKKATPKPEP 266
              + ++     +++D+ +         E 
Sbjct: 61  DAENAMRYINGTRLDDRIIRTDWDAGFKEG 90

>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 = 42.2 bits (99), Expect = 1e-05
 Identities = 16/79 (20%), Positives = 30/79 (37%), Gaps = 5/79 (6%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +    TEE + E FSK G+I+ + +  D     + GF F+ +      E A    +   
Sbjct: 14  NLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA----MRYI 69

Query: 166 GNHVINNKKIEAKKAKAKS 184
               ++++ I         
Sbjct: 70  NGTRLDDRIIRTDWDAGFK 88

>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 = 39.5 bits (92), Expect = 1e-04
 Identities = 13/44 (29%), Positives = 22/44 (50%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E++ E FSK G+I+ + +  D     + GF F+ +      E A
Sbjct: 22  EQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

>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 = 59.7 bits (144), Expect = 8e-12
 Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 11/95 (11%)

Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
           S  +FVG  + +M ++E++  F+Q+G++++  +P        + F F+TF  + +   L 
Sbjct: 5   SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLC 59

Query: 244 KNPKQKINDKEVDVKKATPKPEPFGVRGGRGGRGG 278
                 I    V +  A PK          G   G
Sbjct: 60  GED-LIIKGISVHISNAEPKHN-----SNSGPSSG 88

>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 = 39.6 bits (92), Expect = 7e-05
 Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 12/81 (14%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
                +TE+ L+E FS+YG++ +V           R FAF+ F D +  +          
Sbjct: 12  RCTGDMTEDELREFFSQYGDVMDVF-----IPKPFRAFAFVTFADDQIAQSL------CG 60

Query: 166 GNHVINNKKIEAKKAKAKSGK 186
            + +I    +    A+ K   
Sbjct: 61  EDLIIKGISVHISNAEPKHNS 81

>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 = 37.3 bits (86), Expect = 6e-04
 Identities = 15/79 (18%), Positives = 24/79 (30%), Gaps = 8/79 (10%)

Query: 436 EVTEAVPMEIIET--EMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKK 493
           ++TE    E      ++         + F F+TF  + +   L       I    V +  
Sbjct: 16  DMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGED-LIIKGISVHISN 74

Query: 494 ATPKPEPFGVRGGRGGRGG 512
           A PK          G   G
Sbjct: 75  AEPKHN-----SNSGPSSG 88

>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 = 59.3 bits (143), Expect = 1e-11
 Identities = 19/87 (21%), Positives = 45/87 (51%), Gaps = 3/87 (3%)

Query: 179 KAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESV 238
           ++K+   ++ V  +    +D +++  F QFG I++ E+ +++  S  K F F+TFE+ + 
Sbjct: 6   ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSAD 63

Query: 239 VIDLLKN-PKQKINDKEVDVKKATPKP 264
                +      +  ++++V  AT + 
Sbjct: 64  ADRAREKLHGTVVEGRKIEVNNATARV 90

>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 = 38.1 bits (88), Expect = 3e-04
 Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 7/78 (8%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            I  +  +  L++ F ++G+I +V +  +     S+GF F+ F+++   ++A        
Sbjct: 18  NIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRA----REKL 71

Query: 166 GNHVINNKKIEAKKAKAK 183
              V+  +KIE   A A+
Sbjct: 72  HGTVVEGRKIEVNNATAR 89

>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 = 58.5 bits (141), Expect = 2e-11
 Identities = 17/83 (20%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
           + K+F+GGL   + D+++K     FG +    +  D +    K + F  +   +V    +
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 244 KNP-KQKINDKEVDVKKATPKPE 265
                 ++ DK++ V++A+   +
Sbjct: 61  AGLNGMQLGDKKLLVQRASVGAK 83

>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 = 47.7 bits (113), Expect = 1e-07
 Identities = 17/79 (21%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+ + + ++ +KE  + +G ++   L  D  TG S+G+AF  + D    ++A    +   
Sbjct: 8   GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA----IAGL 63

Query: 166 GNHVINNKKIEAKKAKAKS 184
               + +KK+  ++A   +
Sbjct: 64  NGMQLGDKKLLVQRASVGA 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 = 38.8 bits (90), Expect = 1e-04
 Identities = 13/44 (29%), Positives = 25/44 (56%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +++KE  + +G ++   L  D  TG S+G+AF  + D    ++A
Sbjct: 16  DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 59

>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 = 58.5 bits (141), Expect = 2e-11
 Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 1/84 (1%)

Query: 183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDL 242
           +   ++VGGL  ++ +  +   F Q G ++ T MP D+   Q + + F+ F  E      
Sbjct: 8   QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 243 LKN-PKQKINDKEVDVKKATPKPE 265
           +K     K+  K + V KA+   +
Sbjct: 68  IKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 45.8 bits (108), Expect = 6e-07
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 5/82 (6%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  K++E  L E F + G + N  +  D  TG+ +G+ F+ F   E  + A    +   
Sbjct: 16  GLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA----IKIM 71

Query: 166 GNHVINNKKIEAKKAKAKSGKI 187
               +  K I   KA A +  +
Sbjct: 72  DMIKLYGKPIRVNKASAHNKNL 93

>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 = 35.8 bits (82), Expect = 0.002
 Identities = 13/44 (29%), Positives = 21/44 (47%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
             L E F + G + N  +  D  TG+ +G+ F+ F   E  + A
Sbjct: 24  PLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

>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 = 58.1 bits (140), Expect = 2e-11
 Identities = 14/84 (16%), Positives = 33/84 (39%), Gaps = 4/84 (4%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDK---SKSQRKNFCFITFEHESVVIDLL 243
           +F+  L+    +E +K  F++ G I    +   K          F F+ ++        L
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 244 KNP-KQKINDKEVDVKKATPKPEP 266
           K      ++  +++V+ +    +P
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKP 84

>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 = 48.5 bits (115), Expect = 6e-08
 Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 107 GIVHKITEE-LKEHFSKYGEIEN---VTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV 162
            +    TEE LK  FSK G I++      K+      S GF F+ +K  E  +KA    +
Sbjct: 5   NLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA----L 60

Query: 163 IAEGNHVINNKKIEAKKAKAKS 184
                H ++  K+E + ++  +
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 = 39.2 bits (91), Expect = 1e-04
 Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 3/47 (6%)

Query: 608 EELKEHFSKYGEIEN---VTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           E LK  FSK G I++      K+      S GF F+ +K  E  +KA
Sbjct: 13  ETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 59

>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 = 58.2 bits (140), Expect = 3e-11
 Identities = 24/96 (25%), Positives = 39/96 (40%), Gaps = 5/96 (5%)

Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
           SG++FV  LS    +E+++  F+ +G + E   P D    + K F F+TF      +   
Sbjct: 8   SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAY 67

Query: 244 KN-PKQKINDKEVDVKKATPKPEPFGVRGGRGGRGG 278
                Q    + + V  +T K E        G   G
Sbjct: 68  AEVDGQVFQGRMLHVLPSTIKKE----ASQSGPSSG 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 = 38.2 bits (88), Expect = 4e-04
 Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 5/79 (6%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            + +  +EE L++ FS YG +  +    D  T + +GFAF+ F   E   KA        
Sbjct: 15  NLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA----YAEV 70

Query: 166 GNHVINNKKIEAKKAKAKS 184
              V   + +    +  K 
Sbjct: 71  DGQVFQGRMLHVLPSTIKK 89

>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 = 57.4 bits (138), Expect = 4e-11
 Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            ++VGGL+ E+ D+ + A F  FG+I + ++P D    + + F F+ FE        + N
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 246 P-KQKINDKEVDVKKATPK 263
             + ++  + + V  A P 
Sbjct: 67  MNESELFGRTIRVNLAKPM 85

>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 = 45.0 bits (106), Expect = 1e-06
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 5/81 (6%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+  ++ ++ L   F  +G+I ++ +  D  T + RGFAF+ F+  E    A    +   
Sbjct: 12  GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA----IDNM 67

Query: 166 GNHVINNKKIEAKKAKAKSGK 186
               +  + I    AK    K
Sbjct: 68  NESELFGRTIRVNLAKPMRIK 88

>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 = 34.6 bits (79), Expect = 0.004
 Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           G+ +++ ++ L   F  +G+I ++ +  D  T + RGFAF+ F+  E    A
Sbjct: 12  GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

>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 = 56.9 bits (137), Expect = 5e-11
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            ++VG L P++ +  +   F+  G I+   +  D    +   + ++ F+  +     L  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 246 -PKQKINDKEVDVKKAT 261
                I  K V +  + 
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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 = 49.5 bits (118), Expect = 2e-08
 Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +   +TE  L E FS  G I ++ +  D  T RS G+A++ F+     E+A    +   
Sbjct: 7   DLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA----LDTM 62

Query: 166 GNHVINNKKIEAKKAK 181
              VI  K +    ++
Sbjct: 63  NFDVIKGKPVRIMWSQ 78

>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 = 44.5 bits (105), Expect = 1e-06
 Identities = 15/44 (34%), Positives = 23/44 (52%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
             L E FS  G I ++ +  D  T RS G+A++ F+     E+A
Sbjct: 15  AMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 58

>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 = 56.7 bits (136), Expect = 1e-10
 Identities = 17/90 (18%), Positives = 32/90 (35%), Gaps = 2/90 (2%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
             F+G L  ++ +E IK  F               +  + K F +  FE    ++  L  
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76

Query: 246 PKQKINDKEVDVKKATPKPEPFGVRGGRGG 275
            ++ + +K + V  A    +     G   G
Sbjct: 77  NEESLGNKRIRVDVADQAQDK--DSGPSSG 104

>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 = 37.8 bits (87), Expect = 5e-04
 Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 6/81 (7%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            + + +TEE +KE F           +   N  R +GF +  F+D +SL  A     ++ 
Sbjct: 22  NLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA-----LSL 76

Query: 166 GNHVINNKKIEAKKAKAKSGK 186
               + NK+I    A     K
Sbjct: 77  NEESLGNKRIRVDVADQAQDK 97

>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 = 55.4 bits (133), Expect = 2e-10
 Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 3/86 (3%)

Query: 181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKS-QRKNFCFITFEHESVV 239
           K+  G IF+  L   + ++ +   F+ FGNI+  ++  D++ S       F T E     
Sbjct: 5   KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERA 64

Query: 240 IDLLKNPKQKINDKEVDVKKATPKPE 265
           I+ +      +ND++V V +   + E
Sbjct: 65  IEKMNG--MLLNDRKVFVGRFKSRKE 88

>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 = 37.7 bits (87), Expect = 4e-04
 Identities = 18/79 (22%), Positives = 39/79 (49%), Gaps = 7/79 (8%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +   I  + L + FS +G I +  +  D N   S+G+ F+ F+  E+ E+A    +   
Sbjct: 15  NLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA----IEKM 68

Query: 166 GNHVINNKKIEAKKAKAKS 184
              ++N++K+   + K++ 
Sbjct: 69  NGMLLNDRKVFVGRFKSRK 87

>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 = 55.0 bits (132), Expect = 3e-10
 Identities = 18/78 (23%), Positives = 28/78 (35%), Gaps = 1/78 (1%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            + V  L  +M D E+ A F   G I    +  D        + F+ F  E      +K 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 246 P-KQKINDKEVDVKKATP 262
                + +K + 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 = 43.1 bits (101), Expect = 5e-06
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 4/68 (5%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
            EL   F   G I    +  D  TG S G+AF+ F      ++A    +       + NK
Sbjct: 17  RELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA----IKVLNGITVRNK 72

Query: 174 KIEAKKAK 181
           +++   A+
Sbjct: 73  RLKVSYAR 80

>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 = 37.3 bits (86), Expect = 5e-04
 Identities = 14/44 (31%), Positives = 19/44 (43%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            EL   F   G I    +  D  TG S G+AF+ F      ++A
Sbjct: 17  RELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

>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 = 55.0 bits (132), Expect = 3e-10
 Identities = 15/81 (18%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVV--- 239
           K   ++V  L   + D+++   F ++G+I++  +  DK   + +   F+ +         
Sbjct: 5   KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 240 IDLLKNPKQKINDKEVDVKKA 260
           I  L N   +   + + V+ A
Sbjct: 65  ISALNNVIPEGGSQPLSVRLA 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 = 44.6 bits (105), Expect = 1e-06
 Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
            +   IT++ L   F KYG I    +  D  TGR RG AF+ +   E  ++A
Sbjct: 13  NLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

>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 = 44.6 bits (105), Expect = 1e-06
 Identities = 16/44 (36%), Positives = 23/44 (52%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           ++L   F KYG I    +  D  TGR RG AF+ +   E  ++A
Sbjct: 21  DQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

>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 = 54.8 bits (131), Expect = 4e-10
 Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 2/81 (2%)

Query: 186 KIFVGGLSPEMKDEE-IKAHFAQFGNIIETEMPYDKSKSQR-KNFCFITFEHESVVIDLL 243
           +I +  LS E+ DE  ++  F  FG+I +  +P  + +        F+ FE++      L
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 244 KNPKQKINDKEVDVKKATPKP 264
           +  +  + ++E+ V  A  KP
Sbjct: 66  QMNRSLLGNREISVSLADKKP 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 = 54.0 bits (129), Expect = 7e-10
 Identities = 21/83 (25%), Positives = 45/83 (54%), Gaps = 1/83 (1%)

Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
            GK+FVGGLS +  ++ ++  F+++G I E  +  D+   + + F F+TFE+     D +
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 244 KN-PKQKINDKEVDVKKATPKPE 265
                + ++ +++ V +A    +
Sbjct: 65  MAMNGKSVDGRQIRVDQAGKSSD 87

>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 = 36.6 bits (84), Expect = 9e-04
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 5/79 (6%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+     E+ L++ FSKYG+I  V +  D  T RSRGF F+ F++ +  + A    ++A 
Sbjct: 12  GLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA----MMAM 67

Query: 166 GNHVINNKKIEAKKAKAKS 184
               ++ ++I   +A   S
Sbjct: 68  NGKSVDGRQIRVDQAGKSS 86

>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 = 53.4 bits (128), Expect = 8e-10
 Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK 244
           GK+ V  L   + D +I+  FA+FG + +  + YD+S  +      + FE ++  +  +K
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSG-RSLGTADVHFERKADALKAMK 59

Query: 245 N-PKQKINDKEVDVKKAT 261
                 ++ + ++++  T
Sbjct: 60  QYNGVPLDGRPMNIQLVT 77

>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 = 36.1 bits (83), Expect = 0.001
 Identities = 11/77 (14%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +   +++  ++E F+++G ++   +     +GRS G A + F+      KA    +   
Sbjct: 7   NLDFGVSDADIQELFAEFGTLKKAAVH-YDRSGRSLGTADVHFERKADALKA----MKQY 61

Query: 166 GNHVINNKKIEAKKAKA 182
               ++ + +  +   +
Sbjct: 62  NGVPLDGRPMNIQLVTS 78

>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 = 53.6 bits (128), Expect = 9e-10
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKN-FCFITFE-HESVVIDLLK 244
           IF+G L PE+ ++ +   F+ FG I++T        +     + FI F   ++    +  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 245 NPKQKINDKEVDVKKATPKPE 265
              Q + ++ + V  A  K  
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>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 = 46.7 bits (110), Expect = 2e-07
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 6/82 (7%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVT-LKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIA 164
            +  +I E+ L + FS +G I     +  DP+TG S+G+AFI F   ++ + A    + A
Sbjct: 5   NLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA----IEA 60

Query: 165 EGNHVINNKKIEAKKAKAKSGK 186
                + N+ I    A  K  K
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 36.3 bits (83), Expect = 0.001
 Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 1/45 (2%)

Query: 608 EELKEHFSKYGEIENVT-LKSDPNTGRSRGFAFIVFKDTESLEKA 651
           + L + FS +G I     +  DP+TG S+G+AFI F   ++ + A
Sbjct: 13  KLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 57

>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 = 53.7 bits (128), Expect = 1e-09
 Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 7/87 (8%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            +F+  LS + ++E +     QFG++    +         K   F  F  +      L  
Sbjct: 10  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 69

Query: 246 -------PKQKINDKEVDVKKATPKPE 265
                     K++ +++ V  A  + E
Sbjct: 70  ASLEAEGGGLKLDGRQLKVDLAVTRDE 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 = 36.3 bits (83), Expect = 0.001
 Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA--SVEDVI 163
            +     EE L E   ++G+++ V +   P+T  S+G AF  F   E+ +K   +     
Sbjct: 15  NLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEA 74

Query: 164 AEGNHVINNKKIEAKKAKAKS 184
             G   ++ ++++   A  + 
Sbjct: 75  EGGGLKLDGRQLKVDLAVTRD 95

>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 = 53.1 bits (127), Expect = 1e-09
 Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 4/77 (5%)

Query: 180 AKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVV 239
           A  +   ++V GL   M  +E++  F+Q+G II + +  D+     +   FI F+     
Sbjct: 2   ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 61

Query: 240 IDLLKNPKQKINDKEVD 256
            + +K     +N ++  
Sbjct: 62  EEAIK----GLNGQKPS 74

>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 = 40.0 bits (93), Expect = 6e-05
 Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
           G+   +T++ L++ FS+YG I    +  D  TG SRG  FI F      E+A
Sbjct: 13  GLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

>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 = 39.6 bits (92), Expect = 7e-05
 Identities = 18/44 (40%), Positives = 24/44 (54%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           +EL++ FS+YG I    +  D  TG SRG  FI F      E+A
Sbjct: 21  KELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

>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 = 53.7 bits (129), Expect = 1e-09
 Identities = 14/88 (15%), Positives = 38/88 (43%), Gaps = 10/88 (11%)

Query: 181 KAKSGKIFVGGLSPE-MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVV 239
           ++ + ++F+G L+   +K  +++A F+++G I+   +           F F+ + +E   
Sbjct: 12  RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNA 63

Query: 240 IDLLKN-PKQKINDKEVDVKKATPKPEP 266
              +     + I  + +D+  A      
Sbjct: 64  RAAVAGEDGRMIAGQVLDINLAAEPKVN 91

>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 = 46.0 bits (109), Expect = 5e-07
 Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 12/73 (16%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
            +++  FSKYG+I   ++         +GFAF+ + +  +   A    V  E   +I  +
Sbjct: 31  SDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAA----VAGEDGRMIAGQ 78

Query: 174 KIEAKKAKAKSGK 186
            ++   A      
Sbjct: 79  VLDINLAAEPKVN 91

>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 = 38.7 bits (90), Expect = 2e-04
 Identities = 11/44 (25%), Positives = 22/44 (50%), Gaps = 8/44 (18%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            +++  FSKYG+I   ++         +GFAF+ + +  +   A
Sbjct: 31  SDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAA 66

>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 = 53.3 bits (127), Expect = 2e-09
 Identities = 10/94 (10%), Positives = 26/94 (27%), Gaps = 1/94 (1%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
              +  +   +   ++                   +  Q      + F++E       + 
Sbjct: 10  CAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL 69

Query: 246 PKQKINDKEVDVKKATPK-PEPFGVRGGRGGRGG 278
            ++K+N +E  V   T +            G+ G
Sbjct: 70  HRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSG 103

>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 = 52.7 bits (126), Expect = 2e-09
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
           +  I V  LS + ++ +++  F  FG+I    +  DK+  Q K F FI+F         +
Sbjct: 8   NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 67

Query: 244 KN-PKQKINDKEVDVKKATPK 263
                   +   ++V+ A P 
Sbjct: 68  AGVSGFGYDHLILNVEWAKPS 88

>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 = 40.4 bits (94), Expect = 4e-05
 Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +     E  L+E F  +G I  + L  D  TG+S+GFAFI F   E   +A    +   
Sbjct: 15  NLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA----IAGV 70

Query: 166 GNHVINNKKIEAKKAKAKS 184
                ++  +  + AK  +
Sbjct: 71  SGFGYDHLILNVEWAKPST 89

>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 = 52.7 bits (126), Expect = 2e-09
 Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 3/85 (3%)

Query: 182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVID 241
            +   ++VG LS ++ +  I   F+Q G     +M  +   +    +CF+ F        
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE--HTSNDPYCFVEFYEHRDAAA 63

Query: 242 LLKN-PKQKINDKEVDVKKATPKPE 265
            L     +KI  KEV V  AT    
Sbjct: 64  ALAAMNGRKILGKEVKVNWATTPSS 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 = 38.5 bits (89), Expect = 2e-04
 Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 7/81 (8%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +   +TE  + + FS+ G  ++  + ++     +  + F+ F +      A    + A 
Sbjct: 15  NLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAA----LAAM 68

Query: 166 GNHVINNKKIEAKKAKAKSGK 186
               I  K+++   A   S +
Sbjct: 69  NGRKILGKEVKVNWATTPSSQ 89

>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 = 53.8 bits (128), Expect = 3e-09
 Identities = 17/94 (18%), Positives = 38/94 (40%), Gaps = 1/94 (1%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            + V  +   + + +++  F ++G I   ++  D+   Q + + F+ F+  S     +  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 246 P-KQKINDKEVDVKKATPKPEPFGVRGGRGGRGG 278
                I +K + V  A    +  G+ G  G   G
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIAGAVGDGNG 137

>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 = 51.6 bits (123), Expect = 3e-09
 Identities = 12/82 (14%), Positives = 38/82 (46%), Gaps = 8/82 (9%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK- 244
           K+++G LSP +  ++++  F      +  ++        +  + F+ +  ++  I  ++ 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIET 56

Query: 245 -NPKQKINDKEVDVKKATPKPE 265
            + K +++ K ++V  +  K  
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKL 78

>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 = 37.0 bits (85), Expect = 5e-04
 Identities = 12/81 (14%), Positives = 27/81 (33%), Gaps = 10/81 (12%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +   +T + L++ F                     G+AF+ + D     +A        
Sbjct: 8   NLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIET---LS 58

Query: 166 GNHVINNKKIEAKKAKAKSGK 186
           G   ++ K +E   + +K  +
Sbjct: 59  GKVELHGKIMEVDYSVSKKLR 79

>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 = 51.7 bits (123), Expect = 5e-09
 Identities = 15/93 (16%), Positives = 34/93 (36%), Gaps = 9/93 (9%)

Query: 181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMP--------YDKSKSQRKNFCFIT 232
            + +  I+V GL+  +  +++   F Q G +   +           DK   + K    ++
Sbjct: 5   DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 233 FEHESVVIDLLKNP-KQKINDKEVDVKKATPKP 264
           +E        ++    +     ++ V  A  KP
Sbjct: 65  YEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 97

>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 = 37.1 bits (85), Expect = 0.001
 Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 13/86 (15%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKS--------DPNTGRSRGFAFIVFKDTESLEKA 157
           G+   +T + L + F + G ++              D  TG+ +G A + ++D  + + A
Sbjct: 15  GLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAA 74

Query: 158 SVEDVIAEGNHVINNKKIEAKKAKAK 183
               V           K++   A+ K
Sbjct: 75  ----VEWFDGKDFQGSKLKVSLARKK 96

>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 = 51.9 bits (124), Expect = 6e-09
 Identities = 8/83 (9%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
           +  +++  L  ++  EE+   F ++G I +  +       + +   ++ +E      +  
Sbjct: 7   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNAC 63

Query: 244 KN-PKQKINDKEVDVKKATPKPE 265
            +     + ++ + V        
Sbjct: 64  DHLSGFNVCNRYLVVLYYNANRA 86

>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 = 26/112 (23%), Positives = 48/112 (42%), Gaps = 13/112 (11%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            + +KIT E + + F KYG I  +      NT  +RG A++V++D    + A        
Sbjct: 14  NLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKNA----CDHL 66

Query: 166 GNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMP 217
               + N+ +      A         +  + K+E++K    ++G  I T+ P
Sbjct: 67  SGFNVCNRYLVVLYYNANRAF---QKMDTKKKEEQLKLLKEKYG--INTDPP 113

>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 = 38.8 bits (90), Expect = 3e-04
 Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 3/44 (6%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
           EE+ + F KYG I  +      NT  +RG A++V++D    + A
Sbjct: 22  EEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKNA 62

>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 = 50.6 bits (120), Expect = 9e-09
 Identities = 8/78 (10%), Positives = 22/78 (28%), Gaps = 1/78 (1%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            +++    P      I+        +  +        +  + F +I    +      ++ 
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 246 P-KQKINDKEVDVKKATP 262
               KI    +  K + P
Sbjct: 63  LNGLKIEGYTLVTKVSNP 80

>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 = 50.8 bits (121), Expect = 1e-08
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 14/109 (12%)

Query: 167 NHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRK 226
           +H++ +     K   A+   +    LS  + ++E+K  F          +       + K
Sbjct: 1   SHMLEDPCTSKKVRAAR--TLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSK 53

Query: 227 NFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKPEPFGVRGGRG 274
              +I F+ E+     L+     +I+ + V +     K       G RG
Sbjct: 54  GIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK------GGTRG 96

>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 = 37.7 bits (87), Expect = 5e-04
 Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 10/81 (12%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +   ITE+ LKE F    EI  V        G+S+G A+I FK     EK     +  +
Sbjct: 23  NLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKN----LEEK 73

Query: 166 GNHVINNKKIEAKKAKAKSGK 186
               I+ + +       K G 
Sbjct: 74  QGAEIDGRSVSLYYTGEKGGT 94

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 14/82 (17%), Positives = 32/82 (39%), Gaps = 1/82 (1%)

Query: 179 KAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESV 238
           K   K+  +++ G   +   ++IK      G ++  +M     K   K   F+ F+    
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHK-AFKGSIFVVFDSIES 59

Query: 239 VIDLLKNPKQKINDKEVDVKKA 260
               ++ P QK  + ++ +   
Sbjct: 60  AKKFVETPGQKYKETDLLILFK 81

>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 = 50.1 bits (119), Expect = 2e-08
 Identities = 18/90 (20%), Positives = 43/90 (47%), Gaps = 1/90 (1%)

Query: 177 AKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE 236
           ++K   +   +F+  L  E  D+++   F  FGN++  ++  DK  +  K F F+++++ 
Sbjct: 11  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 70

Query: 237 SVVIDLLKN-PKQKINDKEVDVKKATPKPE 265
                 +++    +I  K + V+    K +
Sbjct: 71  VSAQAAIQSMNGFQIGMKRLKVQLKRSKND 100

>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 = 37.4 bits (86), Expect = 7e-04
 Identities = 13/79 (16%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +  +  ++ L + F  +G + +  +  D  T  S+ F F+ + +  S + A    + + 
Sbjct: 25  HLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA----IQSM 80

Query: 166 GNHVINNKKIEAKKAKAKS 184
               I  K+++ +  ++K+
Sbjct: 81  NGFQIGMKRLKVQLKRSKN 99

>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 = 49.1 bits (116), Expect = 3e-08
 Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 2/76 (2%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            + V  L       ++  +F   G II  ++    S  +   F  I F      +  +  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITK 59

Query: 246 PKQKINDKEVDVKKAT 261
             + +   E+ V   T
Sbjct: 60  THKVVGQNEIIVSHLT 75

>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 = 49.6 bits (117), Expect = 3e-08
 Identities = 15/98 (15%), Positives = 39/98 (39%), Gaps = 7/98 (7%)

Query: 166 GNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQR 225
           G+H++   +            +F+G L+P     E+K   ++     +  +   ++    
Sbjct: 1   GSHMVEGSEST------TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTG-TN 53

Query: 226 KNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           + F ++ FE    +   L+    K+   E+ ++K   +
Sbjct: 54  RKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGR 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 = 36.1 bits (82), Expect = 0.002
 Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 6/70 (8%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
            ELK   S+     ++ +     TG +R F ++ F+  E LEKA     +      +   
Sbjct: 28  AELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKA-----LELTGLKVFGN 81

Query: 174 KIEAKKAKAK 183
           +I+ +K K +
Sbjct: 82  EIKLEKPKGR 91

>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 = 14/78 (17%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN- 245
           +FV  +  E +++EI+  F  +G I    +  D+     K +  + +E     +   +  
Sbjct: 10  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 69

Query: 246 PKQKINDKEVDVKKATPK 263
              +I  + + V     K
Sbjct: 70  NGAEIMGQTIQVDWCFVK 87

>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 = 48.9 bits (116), Expect = 4e-08
 Identities = 16/78 (20%), Positives = 28/78 (35%), Gaps = 1/78 (1%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            + V  L   M  EE ++ F   G I   ++  DK   Q   + F+ +         +  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 246 P-KQKINDKEVDVKKATP 262
               ++  K + V  A P
Sbjct: 64  LNGLRLQTKTIKVSYARP 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 = 39.3 bits (91), Expect = 8e-05
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +   +T+E  +  F   GEIE+  L  D  TG+S G+ F+ + D +  EKA    +   
Sbjct: 9   YLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA----INTL 64

Query: 166 GNHVINNKKIEAKKAK 181
               +  K I+   A+
Sbjct: 65  NGLRLQTKTIKVSYAR 80

>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 = 48.8 bits (116), Expect = 4e-08
 Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 7/88 (7%)

Query: 178 KKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
           +K   +  ++FVG L P++ +EE++  F ++G   E  +         K F FI  E  +
Sbjct: 2   EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFIRLETRT 55

Query: 238 VVIDLLKN-PKQKINDKEVDVKKATPKP 264
           +            +  K++ V+ A    
Sbjct: 56  LAEIAKVELDNMPLRGKQLRVRFACHSA 83

>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 = 35.7 bits (82), Expect = 0.002
 Identities = 18/80 (22%), Positives = 31/80 (38%), Gaps = 11/80 (13%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +   ITEE +++ F KYG+   V +  D        F FI  +     E A     +  
Sbjct: 15  NLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIA----KVEL 64

Query: 166 GNHVINNKKIEAKKAKAKSG 185
            N  +  K++  + A   + 
Sbjct: 65  DNMPLRGKQLRVRFACHSAS 84

>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 = 49.0 bits (116), Expect = 4e-08
 Identities = 11/88 (12%), Positives = 27/88 (30%), Gaps = 5/88 (5%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMP-----YDKSKSQRKNFCFITFEHESVVI 240
           +++VG +   + +E +   F     +                +Q KNF F+ F       
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 241 DLLKNPKQKINDKEVDVKKATPKPEPFG 268
             +         + + +++        G
Sbjct: 63  QAMAFDGIIFQGQSLKIRRPHDYQPLPG 90

>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 = 46.7 bits (110), Expect = 3e-07
 Identities = 13/81 (16%), Positives = 31/81 (38%), Gaps = 11/81 (13%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKS-----DPNTGRSRGFAFIVFKDTESLEKASVE 160
            I   ITEE + + F+    +  +T             + + FAF+ F+  +   +A   
Sbjct: 8   NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA--- 64

Query: 161 DVIAEGNHVINNKKIEAKKAK 181
             +A    +   + ++ ++  
Sbjct: 65  --MAFDGIIFQGQSLKIRRPH 83

>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 = 39.0 bits (90), Expect = 1e-04
 Identities = 8/49 (16%), Positives = 19/49 (38%), Gaps = 5/49 (10%)

Query: 608 EELKEHFSKYGEIENVTLKS-----DPNTGRSRGFAFIVFKDTESLEKA 651
           E + + F+    +  +T             + + FAF+ F+  +   +A
Sbjct: 16  EAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 64

>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 = 49.2 bits (117), Expect = 4e-08
 Identities = 17/99 (17%), Positives = 37/99 (37%), Gaps = 11/99 (11%)

Query: 171 NNKKIE----AKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRK 226
           N K++       ++  K+  ++ GG++  + D+ ++  F+ FG I+E  +         K
Sbjct: 1   NTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP------EK 54

Query: 227 NFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKP 264
            + F+ F         + +     I    V        P
Sbjct: 55  GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP 93

>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 = 36.1 bits (83), Expect = 0.002
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 11/78 (14%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           GI   +T++ +++ FS +G+I  + +         +G++F+ F   ES   A    +++ 
Sbjct: 25  GIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHA----IVSV 74

Query: 166 GNHVINNKKIEAKKAKAK 183
               I    ++    K  
Sbjct: 75  NGTTIEGHVVKCYWGKES 92

>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 = 49.5 bits (117), Expect = 4e-08
 Identities = 14/91 (15%), Positives = 36/91 (39%)

Query: 173 KKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFIT 232
           K+  ++        +++ GL  E +++ +   F +   + ++         +     F+ 
Sbjct: 7   KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVE 66

Query: 233 FEHESVVIDLLKNPKQKINDKEVDVKKATPK 263
           F +E+     L   KQ + ++ + V   T K
Sbjct: 67  FRNEADYKAALCRHKQYMGNRFIQVHPITKK 97

>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 = 36.4 bits (83), Expect = 0.002
 Identities = 11/69 (15%), Positives = 26/69 (37%), Gaps = 5/69 (7%)

Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK 174
            + + F K   +E+    +    G++ G  F+ F++    + A     +      + N+ 
Sbjct: 34  HVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA-----LCRHKQYMGNRF 88

Query: 175 IEAKKAKAK 183
           I+      K
Sbjct: 89  IQVHPITKK 97

>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 = 36.0 bits (82), Expect = 0.002
 Identities = 10/68 (14%), Positives = 23/68 (33%)

Query: 430 TDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEV 489
            +  H+         + ++         +     F+ F +E+     L   KQ + ++ +
Sbjct: 30  AENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFI 89

Query: 490 DVKKATPK 497
            V   T K
Sbjct: 90  QVHPITKK 97

>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 = 49.1 bits (116), Expect = 5e-08
 Identities = 15/84 (17%), Positives = 32/84 (38%)

Query: 181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVI 240
            A  G + + GL      EEI   F+    +          + +     F+ F  + +  
Sbjct: 12  TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAE 71

Query: 241 DLLKNPKQKINDKEVDVKKATPKP 264
             LK  K++I  + +++ K++   
Sbjct: 72  KALKKHKERIGHRYIEIFKSSRAE 95

>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 = 38.3 bits (88), Expect = 4e-04
 Identities = 20/70 (28%), Positives = 29/70 (41%), Gaps = 5/70 (7%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           EE+ + FS    + N         GRS G AF+ F   E  EKA     + +    I ++
Sbjct: 30  EEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKA-----LKKHKERIGHR 84

Query: 174 KIEAKKAKAK 183
            IE  K+   
Sbjct: 85  YIEIFKSSRA 94

>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 = 48.6 bits (115), Expect = 7e-08
 Identities = 14/83 (16%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
           +  +++  LSP + + ++ + FA+F       + +     + +   FITF ++ +    L
Sbjct: 18  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 77

Query: 244 KNP-KQKINDKEVDVKKATPKPE 265
                 K+  K + ++    K +
Sbjct: 78  HLVNGYKLYGKILVIEFGKNKKQ 100

>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 = 48.0 bits (114), Expect = 7e-08
 Identities = 16/79 (20%), Positives = 27/79 (34%), Gaps = 8/79 (10%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            + V G         I   FAQ+GNI++  M          N+  I ++ +      L  
Sbjct: 6   WVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALSK 58

Query: 246 PKQKINDKE-VDVKKATPK 263
             +   +   + VK    K
Sbjct: 59  DGRIFGESIMIGVKPCIDK 77

>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 = 37.6 bits (87), Expect = 3e-04
 Identities = 8/69 (11%), Positives = 20/69 (28%), Gaps = 11/69 (15%)

Query: 107 GIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEG 166
           G        +   F++YG I             +  +  I ++      KA     +++ 
Sbjct: 11  GFPQASASYILLQFAQYGNILKH------VMSNTGNWMHIRYQSKLQARKA-----LSKD 59

Query: 167 NHVINNKKI 175
             +     +
Sbjct: 60  GRIFGESIM 68

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 14/73 (19%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            + V GLS    + +++  F+++G I +  + YD+   + + F F+ FE+     +  + 
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 246 P-KQKINDKEVDV 257
               +++ + + V
Sbjct: 71  ANGMELDGRRIRV 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 = 38.9 bits (90), Expect = 1e-04
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 5/71 (7%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           G+    TE  L+E FSKYG I +V++  D  + RSRGFAF+ F++ +  ++A        
Sbjct: 16  GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA----KERA 71

Query: 166 GNHVINNKKIE 176
               ++ ++I 
Sbjct: 72  NGMELDGRRIR 82

>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 = 35.8 bits (82), Expect = 0.002
 Identities = 19/44 (43%), Positives = 31/44 (70%)

Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
            +L+E FSKYG I +V++  D  + RSRGFAF+ F++ +  ++A
Sbjct: 24  RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

>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 = 12/84 (14%), Positives = 30/84 (35%), Gaps = 2/84 (2%)

Query: 180 AKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVV 239
           A     +I+VG L P+++ ++I+  F ++G I + ++   +         F         
Sbjct: 10  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDA 69

Query: 240 IDLLKNPKQKINDKEVDVKKATPK 263
           +          +   + V+     
Sbjct: 70  VYGRDG--YDYDGYRLRVEFPRSG 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 = 36.2 bits (83), Expect = 0.001
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 8/80 (10%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            +   I  + +++ F KYG I ++ LK+         FAF+ F+D    E A    V   
Sbjct: 21  NLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAEDA----VYGR 73

Query: 166 GNHVINNKKIEAKKAKAKSG 185
             +  +  ++  +  ++  G
Sbjct: 74  DGYDYDGYRLRVEFPRSGRG 93

>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 = 46.9 bits (111), Expect = 2e-07
 Identities = 11/84 (13%), Positives = 31/84 (36%), Gaps = 7/84 (8%)

Query: 182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVID 241
           +    ++V  L     +E I+  F          +       + +++ F+ F +    ++
Sbjct: 6   SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVE 59

Query: 242 LLKN-PKQKINDKEVDVKKATPKP 264
            +K    + ++   ++V  A P  
Sbjct: 60  AMKALNGKVLDGSPIEVTLAKPVD 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 = 35.4 bits (81), Expect = 0.002
 Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 11/78 (14%)

Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
            ++   +EE +++ F+                 + R +AF+ F + E   +A    + A 
Sbjct: 15  NLMLSTSEEMIEKEFNNIKPGAV------ERVKKIRDYAFVHFSNREDAVEA----MKAL 64

Query: 166 GNHVINNKKIEAKKAKAK 183
              V++   IE   AK  
Sbjct: 65  NGKVLDGSPIEVTLAKPV 82

>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 = 47.1 bits (111), Expect = 2e-07
 Identities = 16/92 (17%), Positives = 43/92 (46%), Gaps = 1/92 (1%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            +FVG +  E  +E++K  F++ G ++   + YD+   + K + F  ++ +   +  ++N
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 246 -PKQKINDKEVDVKKATPKPEPFGVRGGRGGR 276
              ++ + + + V  A  +     ++    G 
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKSLGTGA 101

>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 = 45.8 bits (108), Expect = 5e-07
 Identities = 14/85 (16%), Positives = 34/85 (40%), Gaps = 2/85 (2%)

Query: 184 SGKIFVGGLSPEMKDEEIKAH-FAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDL 242
           +  I++  L+ ++K +E+K    A F    +          + +   F+ F+  S   + 
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 243 LKN-PKQKINDKEVDVKKATPKPEP 266
           L++       DK + ++ A    + 
Sbjct: 63  LRSMQGFPFYDKPMRIQYAKTDSDI 87

>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 = 36.6 bits (84), Expect = 9e-04
 Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 12/86 (13%)

Query: 107 GIVHKITEE-----LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED 161
            +  KI ++     L   FS++G+I ++ +         RG AF++FK+  S   A    
Sbjct: 10  NLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---MRGQAFVIFKEVSSATNA---- 62

Query: 162 VIAEGNHVINNKKIEAKKAKAKSGKI 187
           + +       +K +  + AK  S  I
Sbjct: 63  LRSMQGFPFYDKPMRIQYAKTDSDII 88

>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 = 44.3 bits (104), Expect = 2e-06
 Identities = 13/85 (15%), Positives = 25/85 (29%), Gaps = 1/85 (1%)

Query: 177 AKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE 236
           A   K     I V  +   +  +EI   F  +  I  +       K        + FE  
Sbjct: 2   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 61

Query: 237 SVVIDLLKN-PKQKINDKEVDVKKA 260
                 + +   + I  ++V +   
Sbjct: 62  DEATAAVIDLNDRPIGSRKVKLVLG 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 = 36.6 bits (84), Expect = 9e-04
 Identities = 13/67 (19%), Positives = 24/67 (35%), Gaps = 4/67 (5%)

Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
           +E+ + F  Y  I           G   G A + F+  +    A    VI   +  I ++
Sbjct: 24  DEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA----VIDLNDRPIGSR 79

Query: 174 KIEAKKA 180
           K++    
Sbjct: 80  KVKLVLG 86

>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 = 43.6 bits (102), Expect = 4e-06
 Identities = 10/93 (10%), Positives = 25/93 (26%), Gaps = 7/93 (7%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
            + + GL     + +I   F+    +            +      + F      +  +  
Sbjct: 17  CVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGRVTGEADVEFATHEDAVAAMAK 74

Query: 246 PKQKINDKEVDVKKATPKPEPFGVRGGRGGRGG 278
            K  +  + V++   +          G G   G
Sbjct: 75  DKANMQHRYVELFLNSTAG-----TSGSGPSSG 102

>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 = 41.8 bits (98), Expect = 2e-05
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 8/79 (10%)

Query: 106 PGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
           P ++++I E+L+   SK+G+I  +            G A + F+D E  +          
Sbjct: 26  PLVLNEIREDLRVECSKFGQIRKL----LLFDRHPDGVASVSFRDPEEADYCIQT----L 77

Query: 166 GNHVINNKKIEAKKAKAKS 184
                  ++I A+     +
Sbjct: 78  DGRWFGGRQITAQAWDGTT 96

>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 = 39.1 bits (91), Expect = 2e-04
 Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 4/55 (7%)

Query: 600 PGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
           P ++++I E+L+   SK+G+I  +            G A + F+D E  +     
Sbjct: 26  PLVLNEIREDLRVECSKFGQIRKL----LLFDRHPDGVASVSFRDPEEADYCIQT 76

>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 = 41.3 bits (96), Expect = 3e-05
 Identities = 18/95 (18%), Positives = 33/95 (34%), Gaps = 6/95 (6%)

Query: 177 AKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE 236
           AK+ +     +++  L   M ++E++     FG +I T +  D S + R          E
Sbjct: 11  AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTE 70

Query: 237 SVVIDLLKNPKQKINDKEVDVKKATPKP-EPFGVR 270
                  +      N K +        P EP   +
Sbjct: 71  KC-----EAVIGHFNGKFIKTPPGVSAPTEPLLCK 100

>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 = 40.1 bits (93), Expect = 3e-05
 Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
           +++ GL P   D+++      +G I+ T+   DK+ ++ K + F+ F+  S     +   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT-- 58

Query: 247 KQKINDKEVDVKKA 260
              +    V  + A
Sbjct: 59  --ALKASGVQAQMA 70

>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 = 39.4 bits (91), Expect = 1e-04
 Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 4/74 (5%)

Query: 186 KIFVGGLSPEMKDEEIKAHF---AQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDL 242
            +FV GLS  + D E+        +FG I +  +    S +  +      +       D 
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 243 LKNPKQKINDKEVD 256
           L+   Q +N+  VD
Sbjct: 70  LRA-IQCVNNVVVD 82

>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 = 37.7 bits (87), Expect = 4e-04
 Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 3/81 (3%)

Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
           + +++VGGL P      +   F +FG+I   +              + + +        +
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD---SFAYIQYESLDAAQAACAKM 73

Query: 244 KNPKQKINDKEVDVKKATPKP 264
           +       D+ + V  A   P
Sbjct: 74  RGFPLGGPDRRLRVDFAKSGP 94

>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 = 36.0 bits (82), Expect = 0.001
 Identities = 19/94 (20%), Positives = 34/94 (36%), Gaps = 11/94 (11%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           ++ V GL P    +++K H  + G++   ++  D          F+  E  +  +  L N
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----GTGVVEFVRKEDMTYAVRKLDN 57

Query: 246 PKQKINDKEVDVKKATPKPEPFGVRGGRGGRGGR 279
              K    E +      K +     G R    GR
Sbjct: 58  --TKFRSHEGETAYIRVKVD-----GPRSPSYGR 84

>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 = 36.2 bits (83), Expect = 0.002
 Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 2/51 (3%)

Query: 602 IVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
             D+  EE   E   KYGE+E +    D       G  ++ F+  E  EKA
Sbjct: 35  HYDEFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKA 84

>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 = 36.2 bits (83), Expect = 0.002
 Identities = 9/88 (10%), Positives = 27/88 (30%), Gaps = 2/88 (2%)

Query: 172 NKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFI 231
           N    A   ++    + +     E  +E       ++G + E  +  +          ++
Sbjct: 15  NSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYV 73

Query: 232 TFEHESVVIDLLKNP-KQKINDKEVDVK 258
            F  E      + +   +  N + +  +
Sbjct: 74  KFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>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 = 35.8 bits (82), Expect = 0.003
 Identities = 21/72 (29%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 108 IVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEG 166
              +  EE   E   KYGE+E +    D       G  ++ F+  E  EKA    VI   
Sbjct: 35  HYDEFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKA----VIDLN 89

Query: 167 NHVINNKKIEAK 178
           N   N + I A+
Sbjct: 90  NRWFNGQPIHAE 101

>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 = 36.3 bits (83), Expect = 0.002
 Identities = 13/83 (15%), Positives = 28/83 (33%), Gaps = 3/83 (3%)

Query: 182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVID 241
           + S  + V GL   + + ++     +FG I    M   K   ++    F   +     + 
Sbjct: 13  SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK---RQALVEFENIDSAKECVT 69

Query: 242 LLKNPKQKINDKEVDVKKATPKP 264
              +    I  ++     +T K 
Sbjct: 70  FAADVPVYIAGQQAFFNYSTSKR 92

>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 = 35.9 bits (82), Expect = 0.002
 Identities = 10/82 (12%), Positives = 21/82 (25%), Gaps = 6/82 (7%)

Query: 183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDL 242
            S  I V  L  +   +E+      +      +  Y     +      +  E     I +
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYDL----KYCYVDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 243 LKNPKQKINDKEVDVKKATPKP 264
                     K++ V+      
Sbjct: 60  FHQ--YSFRGKDLIVQLQPTDA 79

>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 = 35.5 bits (81), Expect = 0.002
 Identities = 16/92 (17%), Positives = 31/92 (33%), Gaps = 10/92 (10%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
           ++ V GL P    +++K H  + G++   ++  D          ++  E     +  L +
Sbjct: 17  RVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD----GMGMVEYLRKEDMEYALRKLDD 72

Query: 246 PKQKINDKEVDVKKATPKPEPFGVRGGRGGRG 277
              K    E +       PE    R      G
Sbjct: 73  --TKFRSHEGETSYIRVYPE----RSSGPSSG 98

>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 = 35.4 bits (81), Expect = 0.003
 Identities = 7/81 (8%), Positives = 23/81 (28%), Gaps = 7/81 (8%)

Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES---VVIDL 242
           +I V  L   +  + +   F++FG +++       +    +    + +            
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN----QFQALLQYADPVSAQHAKLS 64

Query: 243 LKNPKQKINDKEVDVKKATPK 263
           L           + +  +   
Sbjct: 65  LDGQNIYNACCTLRIDFSKLT 85

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

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 = 35.6 bits (81), Expect = 0.004
 Identities = 12/80 (15%), Positives = 24/80 (30%), Gaps = 2/80 (2%)

Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
            F G L  +   E++   F+  G I   +      +           +          N 
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIIL--FKEKAKEALGKAKDANNG 71

Query: 247 KQKINDKEVDVKKATPKPEP 266
             ++ +KEV  +    + E 
Sbjct: 72  NLQLRNKEVTWEVLEGEVEK 91

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	661
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.95
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.9
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.73
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.73
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.73
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.71
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.71
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.71
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.7
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.7
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.69
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.69
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.68
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.68
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.68
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.68
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.68
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.68
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.67
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.67
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.67
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.67
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.67
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.67
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.67
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.67
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.66
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.66
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.66
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.66
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.65
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.65
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.65
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.65
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.65
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.65
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.65
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.64
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.64
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.64
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.64
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.64
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.63
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.63
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.63
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.63
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.63
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.62
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.62
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.61
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.61
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.61
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.61
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.61
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.6
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.6
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.6
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.59
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.59
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.58
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.58
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.57
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.57
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.57
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.57
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.57
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.57
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.57
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.56
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.56
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.56
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.56
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.56
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.56
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.56
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.56
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.55
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.55
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.54
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.54
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.54
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.53
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.53
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.53
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.53
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.51
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.51
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.51
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.51
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.51
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.51
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.5
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.5
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.5
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.5
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.49
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.49
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.49
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.49
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.49
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.49
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.49
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.48
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.48
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.48
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.48
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.48
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.48
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.48
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.48
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.46
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.46
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.46
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.45
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.45
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.44
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.44
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.43
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.43
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.43
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.42
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.42
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.42
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.42
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.41
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.41
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.4
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.4
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.4
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.39
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.39
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.39
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.39
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.39
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.38
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.38
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.37
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.37
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.36
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.36
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.36
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.36
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.36
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.34
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.34
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.33
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.3
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.27
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.26
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.26
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.26
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.25
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	99.23
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	99.22
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.21
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.2
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.19
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.17
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.16
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.15
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.14
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.11
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.08
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.03
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.95
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.93
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.86
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.82
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.28
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	95.86
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	95.8
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.54
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	95.47
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.33
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.73
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	90.68

>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=2.3e-27  Score=225.20  Aligned_cols=161  Identities=28%  Similarity=0.557  Sum_probs=142.5

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      ++++|.++++++|+++|+++|++||+|.++.+++++.++.++|||||+|.++++|.+|     ....+..+..+.+.+.+
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a-----~~~~~~~~~~~~~~~~~   81 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA-----MNARPHKVDGRVVEPKR   81 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH-----HHTCSCEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHH-----HHhcCCcccccchhhhh
Confidence            4566666666999999999999999999999999999999999999999999999996     55666677777766544


Q ss_pred             hh-----------ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCC
Q psy15852        180 AK-----------AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQ  248 (661)
Q Consensus       180 ~~-----------~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~  248 (661)
                      ..           ...++|||+|||+.+++++|+++|+.||.|..+.++.+..++.++|||||+|.++++|.+||+.+++
T Consensus        82 ~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~  161 (183)
T d1u1qa_          82 AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH  161 (183)
T ss_dssp             CCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCE
T ss_pred             hhhcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCC
Confidence            32           2237999999999999999999999999999999999999999999999999999999999987788


Q ss_pred             ccCCeEEEEEeccCCCC
Q psy15852        249 KINDKEVDVKKATPKPE  265 (661)
Q Consensus       249 ~~~g~~i~V~~a~~k~~  265 (661)
                      .++|++|.|.+|.+|.+
T Consensus       162 ~~~G~~i~V~~A~~k~e  178 (183)
T d1u1qa_         162 TVNGHNCEVRKALSKQE  178 (183)
T ss_dssp             EETTEEEEEEECCCHHH
T ss_pred             eECCEEEEEEecCCccc
Confidence            89999999999987654

>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=99.90  E-value=8.7e-24  Score=200.23  Aligned_cols=173  Identities=22%  Similarity=0.382  Sum_probs=147.1

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKP  264 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k~  264 (661)
                      ++|||+|||+.+|+++|+++|++||.|.++.++++..++.++|||||+|.+.++|.+|+..++..+.++.+.+.+..++.
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~~   86 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSRE   86 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCTT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhcc
Confidence            68999999999999999999999999999999999999999999999999999999999999889999999888776543


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCCCCCCCcccCCCc
Q psy15852        265 EPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLVCRTGPMVQATPPLAEVDVTG  344 (661)
Q Consensus       265 ~~~~~~~~~~~~g~~~g~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (661)
                      .....                                                                   .   .   
T Consensus        87 ~~~~~-------------------------------------------------------------------~---~---   93 (183)
T d1u1qa_          87 DSQRP-------------------------------------------------------------------G---A---   93 (183)
T ss_dssp             GGGST-------------------------------------------------------------------T---T---
T ss_pred             ccccc-------------------------------------------------------------------c---c---
Confidence            21000                                                                   0   0   


Q ss_pred             cEEEEecCCCCCCCCCCCCCCCCChhHHHhhhccccccccccccccccccCCCCCcCccchhhhhhccCcccccCCcccc
Q psy15852        345 VIMILLGAKNHNSDENPTSRSHPSQNAIKLYLTRSSYREWGHVADNLLLCDNFPSIRELEIPEAFLTKTTTVPMTTTEHM  424 (661)
Q Consensus       345 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~l~~~f~~~~~~~~~~~~~~~  424 (661)
                                                              ......+++.++.+.+++++|+.+|..|            
T Consensus        94 ----------------------------------------~~~~~~i~V~~lp~~~te~~L~~~f~~~------------  121 (183)
T d1u1qa_          94 ----------------------------------------HLTVKKIFVGGIKEDTEEHHLRDYFEQY------------  121 (183)
T ss_dssp             ----------------------------------------TCCCSEEEEECCCTTCCHHHHHHHHGGG------------
T ss_pred             ----------------------------------------ccccceeEEccCCCcCCHHHHhhhhccC------------
Confidence                                                    0001234555555569999999999888            


Q ss_pred             hhhcccccccchhhccCCceeEEeeecccccCCcccceEEEEeCChHHHHHHHhCCCCcCCCcEEEEecCCCCCCC
Q psy15852        425 VLVTGTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPEP  500 (661)
Q Consensus       425 ~~~~~~~~~~~~~~~~~~G~i~~~~~~~d~~~~~~~g~aFV~F~~~e~A~~Ai~~~~~~l~g~~i~v~~a~~~~~~  500 (661)
                                        |+|..+.++.|..+++++|||||.|.++++|.+|+.++++.++|+.|.|++|.++.++
T Consensus       122 ------------------G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~~A~~k~e~  179 (183)
T d1u1qa_         122 ------------------GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEM  179 (183)
T ss_dssp             ------------------SCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEETTEEEEEEECCCHHHH
T ss_pred             ------------------CceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeECCEEEEEEecCCcccc
Confidence                              7899999999999999999999999999999999988888899999999999887544

>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=99.73  E-value=4.6e-18  Score=139.86  Aligned_cols=85  Identities=21%  Similarity=0.417  Sum_probs=78.4

Q ss_pred             hhccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEe
Q psy15852        180 AKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKK  259 (661)
Q Consensus       180 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~  259 (661)
                      +..+.++|||+|||+++++++|+++|++||+|.+|.|++|+.+|.++|||||+|.+.++|.+||+. .+.++|+.|.|++
T Consensus         4 ~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~-~~~l~Gr~i~v~~   82 (90)
T d2cqga1           4 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS-CEEETTEEEEEEC
T ss_pred             CCcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc-CCccCCEEeEEEe
Confidence            345568999999999999999999999999999999999999999999999999999999999985 4579999999999


Q ss_pred             ccCCCC
Q psy15852        260 ATPKPE  265 (661)
Q Consensus       260 a~~k~~  265 (661)
                      +.++..
T Consensus        83 a~~k~~   88 (90)
T d2cqga1          83 PNSKQS   88 (90)
T ss_dssp             CCTTCC
T ss_pred             CCCCCC
Confidence            988764

>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=99.73  E-value=1.2e-17  Score=141.37  Aligned_cols=83  Identities=27%  Similarity=0.470  Sum_probs=78.1

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK  263 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k  263 (661)
                      .++|||+|||+.+++++|+++|++||+|.+|.|++++.+++++|||||+|.+.++|++||+.++..+.|++|.|+++..+
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a~~~   89 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLG   89 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEESTTT
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEcCCC
Confidence            46799999999999999999999999999999999999999999999999999999999999988999999999999876


Q ss_pred             CCC
Q psy15852        264 PEP  266 (661)
Q Consensus       264 ~~~  266 (661)
                      ..+
T Consensus        90 ~~p   92 (103)
T d2cqda1          90 AKP   92 (103)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.73  E-value=3.5e-18  Score=140.53  Aligned_cols=67  Identities=28%  Similarity=0.440  Sum_probs=63.3

Q ss_pred             cCCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        591 EAKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       591 ~~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      +..++|||+|||+++||++|+++|++||.|.+|+|++|+.||++||||||+|.++++|.+||++.|.
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~~   72 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHM   72 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEE
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCCc
Confidence            3467899999999999999999999999999999999999999999999999999999999997664

>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=3.3e-18  Score=136.36  Aligned_cols=76  Identities=30%  Similarity=0.523  Sum_probs=73.4

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      |+|||+|||+++++++|+++|++||+|.++.|++|+.+++++|||||+|.+.++|++|++.+++.++|+.|.|+.|
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 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            6899999999999999999999999999999999999999999999999999999999998789999999999986

>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=99.71  E-value=4e-18  Score=135.00  Aligned_cols=64  Identities=31%  Similarity=0.500  Sum_probs=61.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        595 KMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       595 ~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      +|||+|||+++|+++|+++|++||.|.+|+|++|+.||+++|||||+|.+.++|.+||+..+|.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~   64 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHN   64 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCE
Confidence            6999999999999999999999999999999999999999999999999999999999876653

>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=99.71  E-value=3.1e-17  Score=137.79  Aligned_cols=84  Identities=26%  Similarity=0.431  Sum_probs=78.6

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      .+++|||+|||+++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++||+.+ +..|+|+.|+|.++.
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            4578999999999999999999999999999999999999999999999999999999999987 688999999999999


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++.+.
T Consensus        87 ~~~~~   91 (99)
T d1whwa_          87 IKKEA   91 (99)
T ss_dssp             CCSTT
T ss_pred             CCCcc
Confidence            87653

>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=1.5e-17  Score=140.23  Aligned_cols=82  Identities=26%  Similarity=0.488  Sum_probs=78.3

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKP  264 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k~  264 (661)
                      ++|||+|||+++++++|+++|++||.|..+.|++++.++.++|||||+|.+.++|.+||+.+++.|+|+.|.|++|.++.
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~ke  100 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVARE  100 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSCC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECcccC
Confidence            68999999999999999999999999999999999999999999999999999999999888889999999999999887


Q ss_pred             CC
Q psy15852        265 EP  266 (661)
Q Consensus       265 ~~  266 (661)
                      +.
T Consensus       101 ~~  102 (103)
T d1x4ba1         101 ES  102 (103)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.71  E-value=1.7e-17  Score=134.75  Aligned_cols=78  Identities=28%  Similarity=0.533  Sum_probs=75.0

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      .++|||+|||+++++++|+++|++||+|..+.|++++.+++++|||||+|.+.++|++|++.+++.|+|+.|.|+.|.
T Consensus         6 ~~~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           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            368999999999999999999999999999999999999999999999999999999999988899999999999885

>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=1.3e-17  Score=132.30  Aligned_cols=75  Identities=28%  Similarity=0.610  Sum_probs=71.7

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      +|||+|||+++++++|+++|++||+|.+|.+++++.+++++|||||+|.++++|++||+.+++.|+|+.|.|+.|
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 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            599999999999999999999999999999999999999999999999999999999998788999999999764

>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=99.70  E-value=6.1e-18  Score=133.91  Aligned_cols=75  Identities=37%  Similarity=0.758  Sum_probs=72.2

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      +|||+|||+++|+++|+++|++||+|.+|.|++++.+++++|||||+|.+.++|++||+.+++.++|+.|.|+.|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999998889999999999865

>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=99.69  E-value=2.1e-17  Score=133.81  Aligned_cols=79  Identities=23%  Similarity=0.321  Sum_probs=74.8

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      +++|||+|||+++++++|+++|++||+|.+|++++++.++.++|||||+|.++++|++|++.+ +..+.|+.|+|.||+|
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            368999999999999999999999999999999999999999999999999999999999875 7899999999999975

>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=99.69  E-value=3.5e-17  Score=135.62  Aligned_cols=83  Identities=25%  Similarity=0.424  Sum_probs=78.0

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||.++++++|+++|++||+|.+|+|++++.++.++|||||+|.+.++|++|++.+ +..+.|+.|+|++|.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            3579999999999999999999999999999999999999999999999999999999999887 688999999999998


Q ss_pred             CCCC
Q psy15852        262 PKPE  265 (661)
Q Consensus       262 ~k~~  265 (661)
                      ++..
T Consensus        88 ~~~~   91 (93)
T d1x5ua1          88 AHNK   91 (93)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            8753

>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=2.8e-17  Score=130.37  Aligned_cols=65  Identities=43%  Similarity=0.633  Sum_probs=61.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCccc
Q psy15852        595 KMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY  659 (661)
Q Consensus       595 ~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~~  659 (661)
                      +|||+|||+++||++|+++|++||+|.+|+|++|+.||+++|||||+|.++++|++|++..++.+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l   65 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKL   65 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCB
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEE
Confidence            69999999999999999999999999999999999999999999999999999999998755543

>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=99.68  E-value=2.7e-17  Score=135.22  Aligned_cols=81  Identities=26%  Similarity=0.545  Sum_probs=76.6

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      .++|||+|||+++++++|+++|++||+|.+|.+++++.++.++|||||+|.+.++|++|++.+ +..++|+.|.|.++.+
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p   84 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP   84 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            478999999999999999999999999999999999999999999999999999999999875 6889999999999987


Q ss_pred             CC
Q psy15852        263 KP  264 (661)
Q Consensus       263 k~  264 (661)
                      +.
T Consensus        85 ~~   86 (89)
T d2cqba1          85 MR   86 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.68  E-value=7.1e-17  Score=133.74  Aligned_cols=83  Identities=23%  Similarity=0.357  Sum_probs=77.4

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ..+++|||+|||+++++++|+++|++||+|.+|.+++++.++.++|||||+|.+.++|.+|++.+ +..++|++|.|.|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            35689999999999999999999999999999999999999999999999999999999999986 68999999999998


Q ss_pred             cCCC
Q psy15852        261 TPKP  264 (661)
Q Consensus       261 ~~k~  264 (661)
                      ....
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7543

>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=99.68  E-value=1.5e-17  Score=132.57  Aligned_cols=64  Identities=31%  Similarity=0.484  Sum_probs=60.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        594 NKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       594 ~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      ++|||+|||+++||++|+++|++||.|.+|+|++|+.||++||||||+|.+.++|.+|++...+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~   64 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRH   64 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCC
Confidence            5899999999999999999999999999999999999999999999999999999999986433

>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=99.68  E-value=4e-17  Score=132.84  Aligned_cols=79  Identities=22%  Similarity=0.426  Sum_probs=75.5

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCC
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKP  264 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~  264 (661)
                      +|||+|||+++++++|+++|++||+|.+|+|++|+.||.++|||||+|.++++|.+|++.+ +..+.|++|.|.+|.+..
T Consensus         3 rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~   82 (85)
T d2u2fa_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA   82 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            7999999999999999999999999999999999999999999999999999999999987 689999999999998654

>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=99.68  E-value=5.4e-17  Score=130.54  Aligned_cols=76  Identities=17%  Similarity=0.343  Sum_probs=73.1

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      .|||+|||+.+++++|+++|++||+|.+|+|++++.+++++|||||+|.++++|.+|++.+ +..+.|++|+|.|+.
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            6999999999999999999999999999999999999999999999999999999999886 689999999999985

>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=99.67  E-value=5.2e-17  Score=132.20  Aligned_cols=66  Identities=27%  Similarity=0.272  Sum_probs=62.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      ..++|||+|||+++|+++|+++|++||+|.+|+|++|+.+|+++|||||+|.++++|.+|++.+|.
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng   70 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG   70 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCC
Confidence            357899999999999999999999999999999999999999999999999999999999998664

>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=99.67  E-value=5.9e-17  Score=131.13  Aligned_cols=78  Identities=21%  Similarity=0.351  Sum_probs=74.2

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      ++|||+|||+++++++|+++|++||+|.+|+++++..++.++|||||+|.++++|++|++.+ +..+.|+.|.|.+|+|
T Consensus         3 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           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            47999999999999999999999999999999999988999999999999999999999875 7899999999999875

>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=99.67  E-value=6.2e-17  Score=131.32  Aligned_cols=67  Identities=27%  Similarity=0.462  Sum_probs=62.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCccc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY  659 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~~  659 (661)
                      .++|||+|||+++|+++|+++|++||.|.+|+|++|+.||+++|||||+|.++++|.+|++...+.+
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i   72 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKV   72 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEE
Confidence            3689999999999999999999999999999999999999999999999999999999998765543

>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=99.67  E-value=3.7e-17  Score=132.35  Aligned_cols=79  Identities=23%  Similarity=0.322  Sum_probs=72.2

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ++.|||+|+| ++++++|+++|++||+|.+|+|++++.+|+++|||||+|.++++|++|    +..+|+..+.|++|.|.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~a----i~~lng~~~~g~~l~v~   77 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA----IKVLNGITVRNKRLKVS   77 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHH----HHHhCCCEECCEEEEEE
Confidence            3445555555 999999999999999999999999999999999999999999999999    88999999999999999


Q ss_pred             hhhc
Q psy15852        179 KAKA  182 (661)
Q Consensus       179 ~~~~  182 (661)
                      +++|
T Consensus        78 ~a~p   81 (82)
T d1b7fa1          78 YARP   81 (82)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            9875

>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=99.67  E-value=5.1e-17  Score=133.20  Aligned_cols=80  Identities=18%  Similarity=0.358  Sum_probs=75.9

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      .++|||+|||.++++++|+++|++||+|.+|++++++.+|+++|||||+|.+.++|++|++.+ +..+.|+.|.|.||.+
T Consensus         7 ~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~   86 (88)
T d1rk8a_           7 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV   86 (88)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecC
Confidence            468999999999999999999999999999999999999999999999999999999999875 7899999999999987


Q ss_pred             C
Q psy15852        263 K  263 (661)
Q Consensus       263 k  263 (661)
                      +
T Consensus        87 k   87 (88)
T d1rk8a_          87 K   87 (88)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.67  E-value=8.3e-17  Score=144.19  Aligned_cols=82  Identities=16%  Similarity=0.328  Sum_probs=77.2

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ++|||+|||+++++++|+++|++||+|.+|.|++++.+++++|||||+|.+.++|.+||+.+ +..|+|+.|.|.++.++
T Consensus        43 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~  122 (139)
T d1u6fa1          43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASG  122 (139)
T ss_dssp             SEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            68999999999999999999999999999999999999999999999999999999999986 68999999999999876


Q ss_pred             CCC
Q psy15852        264 PEP  266 (661)
Q Consensus       264 ~~~  266 (661)
                      ..+
T Consensus       123 ~~~  125 (139)
T d1u6fa1         123 HQR  125 (139)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=1e-16  Score=128.65  Aligned_cols=76  Identities=28%  Similarity=0.593  Sum_probs=73.2

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      ++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.++++|.+|++.+++.|+|+.|.|+.|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            6899999999999999999999999999999999999999999999999999999999987789999999999986

>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=99.67  E-value=6.6e-17  Score=133.18  Aligned_cols=82  Identities=23%  Similarity=0.379  Sum_probs=77.3

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||.++++++|+++|++||+|.+|.++.++.++.++|||||+|.+.++|.+|++.+ +..++|+.|.|.||.
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            3578999999999999999999999999999999999999999999999999999999999987 689999999999998


Q ss_pred             CCC
Q psy15852        262 PKP  264 (661)
Q Consensus       262 ~k~  264 (661)
                      ++.
T Consensus        87 p~~   89 (90)
T d2cq0a1          87 PST   89 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.66  E-value=8.1e-17  Score=131.13  Aligned_cols=66  Identities=24%  Similarity=0.327  Sum_probs=62.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      .++|||+|||++++|++|+++|++||.|.+|+|++|+.+|+++|||||+|.++++|.+|++++|..
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   71 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNV   71 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCC
Confidence            568999999999999999999999999999999999999999999999999999999999987653

>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=99.66  E-value=9.7e-17  Score=129.84  Aligned_cols=79  Identities=27%  Similarity=0.383  Sum_probs=72.2

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ++.||++|+| ++++++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|    +..+++..+.|++|.|.
T Consensus         2 ~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           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA----INTLNGLRLQTKTIKVS   77 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHH----HHHhCCCEECCEEEEEE
Confidence            3445555555 999999999999999999999999999999999999999999999999    88999999999999999


Q ss_pred             hhhc
Q psy15852        179 KAKA  182 (661)
Q Consensus       179 ~~~~  182 (661)
                      +++|
T Consensus        78 ~AkP   81 (82)
T d1fxla1          78 YARP   81 (82)
T ss_dssp             ECCC
T ss_pred             EeeC
Confidence            9875

>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=99.66  E-value=7e-17  Score=136.24  Aligned_cols=84  Identities=20%  Similarity=0.398  Sum_probs=78.7

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ++.++|||+|||+++++++|+++|++||.|.++.++.++.++.++|||||+|.+.++|.+||+.+ +..|.|++|.|+|+
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            44578999999999999999999999999999999999999999999999999999999999875 78999999999999


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .++.+
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            98765

>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=99.66  E-value=6.3e-17  Score=134.09  Aligned_cols=82  Identities=24%  Similarity=0.298  Sum_probs=74.4

Q ss_pred             cEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        101 KMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       101 ~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +.||++|+| ++++++|+++|++||+|.+|+|++++.||.+||||||+|.+.++|++|    +..+++..+.|++|.|.+
T Consensus        10 ~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~A----i~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1          10 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA----IKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHH----HHHSSSCBCSSCBCEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHH----HHHcCCCEECCEEEEEEE
Confidence            445555554 999999999999999999999999999999999999999999999999    889999999999999999


Q ss_pred             hhccCCe
Q psy15852        180 AKAKSGK  186 (661)
Q Consensus       180 ~~~~~~~  186 (661)
                      +.++.++
T Consensus        86 A~~~~~n   92 (93)
T d1x5ua1          86 ASAHNKN   92 (93)
T ss_dssp             TTTTSCC
T ss_pred             cCCCCCC
Confidence            9887654

>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=99.65  E-value=1.3e-16  Score=129.41  Aligned_cols=79  Identities=25%  Similarity=0.454  Sum_probs=73.4

Q ss_pred             eEecCCCccCCHHHHHHHHhcCCCeEEE-EeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCCC
Q psy15852        187 IFVGGLSPEMKDEEIKAHFAQFGNIIET-EMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPKP  264 (661)
Q Consensus       187 lfV~nLp~~~te~~L~~~F~~~G~i~~v-~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k~  264 (661)
                      |||+|||+++++++|+++|++||.|.++ .+++++.+++++|||||+|.+.++|.+|++.+ +..++|++|.|.++.++.
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            7999999999999999999999998664 78999999999999999999999999999876 689999999999999876


Q ss_pred             C
Q psy15852        265 E  265 (661)
Q Consensus       265 ~  265 (661)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.65  E-value=8.6e-17  Score=130.39  Aligned_cols=66  Identities=29%  Similarity=0.437  Sum_probs=62.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      .++|||+|||+++||++|+++|++||.|.+|+|++|+.||+++|||||+|.+.++|.+|++++|..
T Consensus         9 ~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~   74 (83)
T d2cqca1           9 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM   74 (83)
T ss_dssp             GGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCC
Confidence            468999999999999999999999999999999999999999999999999999999999976643

>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=99.65  E-value=1.4e-16  Score=134.68  Aligned_cols=66  Identities=24%  Similarity=0.420  Sum_probs=63.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      .++|||+|||+++||+||+++|++||.|.+|+|++|+.||+++|||||+|.+.++|.+||+.+++.
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~   75 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPI   75 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCE
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCc
Confidence            468999999999999999999999999999999999999999999999999999999999987754

>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=99.65  E-value=4.4e-17  Score=133.97  Aligned_cols=81  Identities=22%  Similarity=0.293  Sum_probs=73.4

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ++++++.++++++++++|+++|++||+|.+|+|++++.+|++||||||+|.++++|++|    +..+++..+.|++|.|.
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~a----i~~l~~~~i~g~~l~v~   80 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA----IDNMNESELFGRTIRVN   80 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHH----HHHHTTEEETTEEEEEE
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHH----HHHcCCCEECCEEEEEE
Confidence            34555555555999999999999999999999999999999999999999999999999    88999999999999999


Q ss_pred             hhhcc
Q psy15852        179 KAKAK  183 (661)
Q Consensus       179 ~~~~~  183 (661)
                      ++.++
T Consensus        81 ~a~p~   85 (89)
T d2cqba1          81 LAKPM   85 (89)
T ss_dssp             ECCCC
T ss_pred             EeCCC
Confidence            98765

>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=99.65  E-value=1.3e-16  Score=129.91  Aligned_cols=79  Identities=25%  Similarity=0.457  Sum_probs=72.7

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC--eEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND--KEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g--~~i~V~  258 (661)
                      .+.++|||+|||+.+++++|+++|++||+|.++++++++.++.++|||||+|.++++|.+|++.+ +..+.|  ++|.|+
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            35678999999999999999999999999999999999999999999999999999999999876 678887  569998


Q ss_pred             ec
Q psy15852        259 KA  260 (661)
Q Consensus       259 ~a  260 (661)
                      ||
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.65  E-value=1.4e-16  Score=130.55  Aligned_cols=80  Identities=26%  Similarity=0.375  Sum_probs=72.7

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++|++|+| ++++++|+++|++||+|.+|+|++++.+|++||||||+|.+.++|++|    +..+|+..+.|+.|.|.
T Consensus         7 ~~~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_           7 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA----KEALNGAEIMGQTIQVD   82 (88)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHH----HHHcCCCEECCEEEEEE
Confidence            3455555555 999999999999999999999999999999999999999999999999    88999999999999999


Q ss_pred             hhhcc
Q psy15852        179 KAKAK  183 (661)
Q Consensus       179 ~~~~~  183 (661)
                      ++.++
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            98764

>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=99.65  E-value=1.1e-16  Score=131.90  Aligned_cols=84  Identities=25%  Similarity=0.519  Sum_probs=78.0

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||+++++++|+++|++||.|..+.++++..++.++|||||+|.++++|++|++.+ +..++|++|.|++|.
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            3578999999999999999999999999999999999999999999999999999999999875 789999999999998


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++...
T Consensus        84 ~~~~~   88 (90)
T d1x5sa1          84 KSSDN   88 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87643

>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=99.64  E-value=9.4e-17  Score=134.91  Aligned_cols=80  Identities=13%  Similarity=0.278  Sum_probs=75.6

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK  263 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k  263 (661)
                      .++|||+|||+++++++|+++|++||+|.+|.|+++..+|+++|||||+|.+.++|.+|++.++..|.|+.|.|+++.++
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~~~   97 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAE   97 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECCCC
Confidence            36899999999999999999999999999999999999999999999999999999999987788999999999998654

>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=99.64  E-value=1e-16  Score=130.38  Aligned_cols=81  Identities=21%  Similarity=0.343  Sum_probs=75.1

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++|+++|+++|++||+|.+|+|++|+.||++||||||+|.++++|.+|    +..+++..|.|++|.|.+
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a----~~~l~~~~l~g~~l~V~~   77 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA----IAGLNGMQLGDKKLLVQR   77 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHH----HHTSSSCCCSSSCCEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHH----HHHhCCCEECCEEEEEEE
Confidence            4677777777999999999999999999999999999999999999999999999999    888999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.+..
T Consensus        78 A~~~~   82 (85)
T d2u2fa_          78 ASVGA   82 (85)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.64  E-value=2.1e-16  Score=126.27  Aligned_cols=76  Identities=20%  Similarity=0.416  Sum_probs=71.4

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      +|||+|||+++++++|+++|++||+|.+|+++.++ +++++|||||+|.+.++|++|++.+ +..++|++|.|+++.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            69999999999999999999999999999999886 6899999999999999999999875 7899999999999863

>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=99.64  E-value=2.5e-16  Score=130.65  Aligned_cols=83  Identities=16%  Similarity=0.328  Sum_probs=75.8

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCC-CCCCcCcEEEEEeCCHHHHHHHHHhC--CCccCCeEEEEEe
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDK-SKSQRKNFCFITFEHESVVIDLLKNP--KQKINDKEVDVKK  259 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~Al~~~--~~~~~g~~i~V~~  259 (661)
                      ..++|||+|||+++++++|+++|++||.|.+|.|+++. .+|+++|||||+|.+.++|.+|++.+  +..+.|++|.|.|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            45789999999999999999999999999999999875 47999999999999999999999975  5789999999999


Q ss_pred             ccCCCC
Q psy15852        260 ATPKPE  265 (661)
Q Consensus       260 a~~k~~  265 (661)
                      |.++..
T Consensus        87 A~~~~~   92 (94)
T d2cpha1          87 ADSEVT   92 (94)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            987653

>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=99.64  E-value=1.5e-16  Score=128.29  Aligned_cols=78  Identities=10%  Similarity=0.158  Sum_probs=67.6

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      ++|||+|||+++++++|+++|++||.|..+.++.+..+++++|||||+|.+.++|++|++.+ +..++|++|.|+++.|
T Consensus         2 ~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           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            68999999999999999999999999999988888888999999999999999999999875 7899999999999976

>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=99.64  E-value=1.8e-16  Score=125.90  Aligned_cols=75  Identities=40%  Similarity=0.655  Sum_probs=71.8

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      +|||+|||+++|+++|+++|++||.|..+.++.++.++.+++||||+|.+.++|++|++.+++.|+|++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999986689999999999986

>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=99.63  E-value=2.2e-16  Score=128.53  Aligned_cols=78  Identities=15%  Similarity=0.393  Sum_probs=72.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC--eEEEEEe
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND--KEVDVKK  259 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g--~~i~V~~  259 (661)
                      +.++|||+|||+++++++|+++|++||+|.++++++++.+++++|||||+|.++++|.+|++.+ +..+.|  ++|.|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            3468999999999999999999999999999999999999999999999999999999999986 566765  8899998


Q ss_pred             c
Q psy15852        260 A  260 (661)
Q Consensus       260 a  260 (661)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.63  E-value=1.8e-16  Score=130.58  Aligned_cols=80  Identities=25%  Similarity=0.433  Sum_probs=72.9

Q ss_pred             cEEEEcCC-CcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        101 KMVSHPGI-VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       101 ~~~~~~~~-~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +.|+++|+ +++++++|+++|++||+|.+|+|++++.+|++||||||+|.+.++|++|    +..+++..+.|+.|.|.+
T Consensus         9 ~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~A----i~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           9 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA----IAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             EEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHH----HHHTTTCEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHH----HHHhCCCEECCEEEEEEe
Confidence            34555555 5999999999999999999999999999999999999999999999999    899999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +++++
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            98764

>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=99.63  E-value=2e-16  Score=128.93  Aligned_cols=81  Identities=25%  Similarity=0.452  Sum_probs=70.4

Q ss_pred             CCeeEecCCCccCC-HHHHHHHHhcCCCeEEEEeccC-CCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        184 SGKIFVGGLSPEMK-DEEIKAHFAQFGNIIETEMPYD-KSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       184 ~~~lfV~nLp~~~t-e~~L~~~F~~~G~i~~v~i~~~-~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      .++|||+|||++++ +++|+++|++||.|.+|.|+.+ ..+++++|||||+|.+.++|.+|++.++..++|+.|+|+++.
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a~   83 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLAD   83 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEECC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEcC
Confidence            47899999999976 5669999999999999998764 467899999999999999999999866889999999999998


Q ss_pred             CCC
Q psy15852        262 PKP  264 (661)
Q Consensus       262 ~k~  264 (661)
                      +++
T Consensus        84 ~kP   86 (86)
T d2ghpa3          84 KKP   86 (86)
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=99.63  E-value=2.5e-16  Score=128.21  Aligned_cols=78  Identities=18%  Similarity=0.373  Sum_probs=71.3

Q ss_pred             eEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCC---CcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKS---QRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       187 lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g---~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      |||+|||+++++++|+++|++||+|.+|.|++++.++   .++|||||+|.+.++|.+|++.+ +..++|+.|.|+++.+
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            7999999999999999999999999999999887664   56899999999999999999886 6899999999999875


Q ss_pred             CC
Q psy15852        263 KP  264 (661)
Q Consensus       263 k~  264 (661)
                      +.
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            44

>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=99.63  E-value=2.6e-16  Score=126.50  Aligned_cols=76  Identities=24%  Similarity=0.255  Sum_probs=70.1

Q ss_pred             EEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhh
Q psy15852        102 MVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAK  181 (661)
Q Consensus       102 ~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~  181 (661)
                      +++.++++++|+++|+++|++||+|.+|+|++++.||+++|||||+|.++++|.+|    +..+++..+.|++|.|.+++
T Consensus         3 lfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~a----i~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           3 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA----LDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH----HTTSTTCEETTEECEEEECC
T ss_pred             EEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHH----HHHcCCCEECCEEEEEEEeC
Confidence            44555555999999999999999999999999999999999999999999999999    88999999999999998875

>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=99.62  E-value=1.8e-16  Score=134.35  Aligned_cols=80  Identities=19%  Similarity=0.498  Sum_probs=75.9

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ++|||+|||+++++++|+++|++||+|.+|.+++++.+|+++|||||+|.+.++|.+|++.+ +..+.|+.|.|.++.++
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            68999999999999999999999999999999999999999999999999999999999986 68999999999998875


Q ss_pred             C
Q psy15852        264 P  264 (661)
Q Consensus       264 ~  264 (661)
                      .
T Consensus        89 ~   89 (104)
T d1p1ta_          89 K   89 (104)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.62  E-value=4.6e-16  Score=127.75  Aligned_cols=80  Identities=24%  Similarity=0.477  Sum_probs=73.6

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      ..+|||+|||+++++++|+++|++||.|..+.|+.+..  .++|||||+|.+.++|++|++.+ +..++|+.|.|.++.+
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 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            46899999999999999999999999999999998864  47899999999999999999887 6899999999999998


Q ss_pred             CCC
Q psy15852        263 KPE  265 (661)
Q Consensus       263 k~~  265 (661)
                      +.+
T Consensus        86 ~~~   88 (89)
T d1cvja2          86 RKE   88 (89)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            764

>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=99.61  E-value=7.3e-16  Score=124.79  Aligned_cols=75  Identities=27%  Similarity=0.451  Sum_probs=68.5

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ..++++.+|++++|+++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+++..+.|++|.|
T Consensus         9 ~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A----i~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           9 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA----KERANGMELDGRRIRV   83 (83)
T ss_dssp             GGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHH----HHHHTTEEETTEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHH----HHHcCCCEECCEEeEC
Confidence            44566666666999999999999999999999999999999999999999999999999    8899999999999875

>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=99.61  E-value=6.3e-16  Score=127.93  Aligned_cols=80  Identities=18%  Similarity=0.240  Sum_probs=71.8

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..++++.++++++|+++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|.+|    +..+|+..+.|++|.|.
T Consensus         7 s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~A----i~~l~g~~~~gr~i~V~   82 (93)
T d1h2vz_           7 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA----MRYINGTRLDDRIIRTD   82 (93)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH----HHHTTTSEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHH----HHHhCCCEECCEEEEEE
Confidence            34444555555999999999999999999999999999999999999999999999999    88999999999999999


Q ss_pred             hhhc
Q psy15852        179 KAKA  182 (661)
Q Consensus       179 ~~~~  182 (661)
                      ++..
T Consensus        83 ~a~~   86 (93)
T d1h2vz_          83 WDAG   86 (93)
T ss_dssp             EESC
T ss_pred             EcCC
Confidence            8753

>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=99.61  E-value=9.7e-16  Score=126.05  Aligned_cols=82  Identities=26%  Similarity=0.389  Sum_probs=73.8

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ...++|||+|||.++++++|+++|++||+|.+|.++++..+  .++||||+|.+.++|.+|++.+ +..+.|+.|+|.||
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            34579999999999999999999999999999999988754  4899999999999999999875 67899999999999


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .++..
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            87543

>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=99.61  E-value=9.3e-16  Score=124.55  Aligned_cols=78  Identities=15%  Similarity=0.330  Sum_probs=72.6

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      +.++|||+|||.++++++|+++|++||+|..|.++.+. +++++|||||+|.++++|.+||+..+..+.|+.|.|.+..
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-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            35789999999999999999999999999999998775 6899999999999999999999887899999999999865

>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=99.61  E-value=3.2e-16  Score=131.63  Aligned_cols=79  Identities=22%  Similarity=0.346  Sum_probs=71.2

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +++++.++++++++++|+++|+.||+|.+|+|++++.+|++||||||+|.+.++|.+|    + .+++..|.|+.|.|.+
T Consensus        19 ~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A----~-~l~g~~~~G~~l~V~~   93 (101)
T d2cq4a1          19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA----I-GLTGQRLLGVPIIVQA   93 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHH----H-HHTTEEETTEEEEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHH----H-HHCCCEECCEEEEEEE
Confidence            4555555556999999999999999999999999999999999999999999999997    6 6999999999999998


Q ss_pred             hhcc
Q psy15852        180 AKAK  183 (661)
Q Consensus       180 ~~~~  183 (661)
                      +.++
T Consensus        94 a~~~   97 (101)
T d2cq4a1          94 SQAE   97 (101)
T ss_dssp             HHHH
T ss_pred             CCCC
Confidence            7654

>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=99.60  E-value=1.2e-15  Score=127.91  Aligned_cols=83  Identities=18%  Similarity=0.336  Sum_probs=76.5

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-------CCccCCeEE
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-------KQKINDKEV  255 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-------~~~~~g~~i  255 (661)
                      ..++|||+|||+++++++|+++|++||+|.++.++.+..++.++|||||+|.+.++|.+||+.+       +..+.|+.|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l   86 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   86 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEE
Confidence            3578999999999999999999999999999999999999999999999999999999999874       356899999


Q ss_pred             EEEeccCCCC
Q psy15852        256 DVKKATPKPE  265 (661)
Q Consensus       256 ~V~~a~~k~~  265 (661)
                      .|.++.++.+
T Consensus        87 ~v~~a~~k~~   96 (98)
T d1x4ha1          87 KVDLAVTRDE   96 (98)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEECCCCCc
Confidence            9999998764

>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=99.60  E-value=1.3e-15  Score=125.95  Aligned_cols=81  Identities=21%  Similarity=0.464  Sum_probs=74.0

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||+++++++|+++|++||+|.+|.++.+..  .++|||||+|.++++|.+|++.+ +..++|+.|.|.+|.
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            357899999999999999999999999999999998864  46999999999999999999875 789999999999999


Q ss_pred             CCCC
Q psy15852        262 PKPE  265 (661)
Q Consensus       262 ~k~~  265 (661)
                      ++..
T Consensus        88 ~r~~   91 (93)
T d2cq3a1          88 ARVM   91 (93)
T ss_dssp             SSCC
T ss_pred             cCCC
Confidence            8753

>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=99.60  E-value=6.8e-16  Score=129.45  Aligned_cols=81  Identities=22%  Similarity=0.344  Sum_probs=73.4

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .+++|.++++++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|    +..+|+..|.|++|.|.+
T Consensus         9 ~~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_           9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA----YAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHH----HHHTTTEESSSCEEEEEE
T ss_pred             CEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHH----HHHcCCCEECCEEEEEEE
Confidence            4455555556999999999999999999999999999999999999999999999999    889999999999999998


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        85 a~~~~   89 (99)
T d1whwa_          85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            87653

>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=99.60  E-value=8.3e-16  Score=129.52  Aligned_cols=82  Identities=16%  Similarity=0.241  Sum_probs=74.6

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..+|+|.++++++++++|+++|++||+|.+|+++.++.+|++||||||+|.++++|++|    +..+|+..|.|++|.|.
T Consensus        18 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~A----i~~lng~~~~g~~i~V~   93 (102)
T d2cpza1          18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA----IQSMNGFQIGMKRLKVQ   93 (102)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHH----HHHhCCCEECCEEEEEE
Confidence            34555566666999999999999999999999999999999999999999999999999    88999999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        94 ~a~~k~   99 (102)
T d2cpza1          94 LKRSKN   99 (102)
T ss_dssp             CCCCSC
T ss_pred             EeCCCC
Confidence            998764

>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=99.59  E-value=8.9e-16  Score=127.27  Aligned_cols=83  Identities=24%  Similarity=0.380  Sum_probs=73.4

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCC-CCCcccEEEEEEeehhhHHHhhHHHHHHh-CCeeecceee
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPN-TGRSRGFAFIVFKDTESLEKASVEDVIAE-GNHVINNKKI  175 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~-tg~srG~afV~F~~~e~A~~A~~~~~~~~-~~~~i~g~~i  175 (661)
                      ...++++.++++++++++|+++|++||+|.+|+|+++.. +|++||||||+|.+.++|.+|    +..+ |+..+.|++|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~A----i~~l~~~~~~~Gr~l   82 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA----FNALCHSTHLYGRRL   82 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHH----HHHHHTCCBSSSCBC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHH----HHHccCCcEECCEEE
Confidence            445666666666999999999999999999999998754 799999999999999999999    8887 8999999999


Q ss_pred             hhhhhhccC
Q psy15852        176 EAKKAKAKS  184 (661)
Q Consensus       176 ~v~~~~~~~  184 (661)
                      .|.++.++.
T Consensus        83 ~V~~A~~~~   91 (94)
T d2cpha1          83 VLEWADSEV   91 (94)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEcCCCC
Confidence            999997654

>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=5.7e-16  Score=121.82  Aligned_cols=63  Identities=17%  Similarity=0.238  Sum_probs=60.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        596 MVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       596 l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      |||+|||+++|+++|+++|++||.|..+++++++.+++++|||||+|.++++|.+|++.+|..
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~   63 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKAS   63 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCC
Confidence            799999999999999999999999999999999999999999999999999999999987653

>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=99.58  E-value=1.1e-15  Score=121.97  Aligned_cols=76  Identities=17%  Similarity=0.272  Sum_probs=69.5

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      ++++.++++++++++|+++|++||+|.+|+|+.++ +|+++|||||+|.++++|.+|    +..+|+..+.|++|.|.++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~A----i~~l~g~~l~g~~l~V~~a   76 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKA----MKQYNGVPLDGRPMNIQLV   76 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHH----HHHHTTCEETTEECEEEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHH----HHHhCCCEECCEEEEEEEe
Confidence            46666666799999999999999999999999986 699999999999999999999    8899999999999999876


Q ss_pred             h
Q psy15852        181 K  181 (661)
Q Consensus       181 ~  181 (661)
                      .
T Consensus        77 ~   77 (78)
T d1no8a_          77 T   77 (78)
T ss_dssp             C
T ss_pred             e
Confidence            4

>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=99.58  E-value=1.7e-15  Score=126.16  Aligned_cols=82  Identities=18%  Similarity=0.366  Sum_probs=74.0

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCC-eEEEEeccCC-CCCCcCcEEEEEeCCHHHHHHHHHhC---CCccCCeEEEEEe
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGN-IIETEMPYDK-SKSQRKNFCFITFEHESVVIDLLKNP---KQKINDKEVDVKK  259 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~-i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~Al~~~---~~~~~g~~i~V~~  259 (661)
                      |+|||+|||.++++++|+++|++||+ |..+.++++. .+++++|||||+|.++++|.+|++.+   +..+.|+.|.|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            68999999999999999999999996 9999999875 46889999999999999999999986   3467899999999


Q ss_pred             ccCCCCC
Q psy15852        260 ATPKPEP  266 (661)
Q Consensus       260 a~~k~~~  266 (661)
                      |.++.++
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9987754

>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=99.57  E-value=4.4e-15  Score=125.68  Aligned_cols=83  Identities=20%  Similarity=0.388  Sum_probs=73.6

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCC-CCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDK-SKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      +.++|||+|||+++++++|+++|++|| |..+.++.+. .+++++|||||+|.+.++|++|++.++..|+|+.|+|.++.
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a~   92 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVAD   92 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            457999999999999999999999999 7778777665 46889999999999999999888767899999999999998


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++...
T Consensus        93 ~~~~~   97 (104)
T d1wi8a_          93 QAQDK   97 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77643

>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=99.57  E-value=1e-15  Score=129.57  Aligned_cols=80  Identities=20%  Similarity=0.337  Sum_probs=72.9

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +++++.++++++++++|+++|++||+|.+|+|++++.||+++|||||+|.+.++|++|    +..+++..|.|++|.|.+
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~a----i~~l~~~~~~g~~i~V~~   84 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA----MRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHH----HHHSSSBSCSSSCBEEEE
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHH----HHHcCCCEECCEEEEEEE
Confidence            4566666666999999999999999999999999999999999999999999999999    889999999999999988


Q ss_pred             hhcc
Q psy15852        180 AKAK  183 (661)
Q Consensus       180 ~~~~  183 (661)
                      +.++
T Consensus        85 a~~~   88 (104)
T d1p1ta_          85 AASE   88 (104)
T ss_dssp             TTCT
T ss_pred             CCCC
Confidence            7653

>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=99.57  E-value=2.8e-15  Score=121.69  Aligned_cols=63  Identities=19%  Similarity=0.257  Sum_probs=58.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      .++|||+|||+++|+++|+++|+.||+|.+|+|++++ +|+++|||||+|.++++|.+|++...
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~   68 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG   68 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCC
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCC
Confidence            5789999999999999999999999999999998876 69999999999999999999997543

>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=99.57  E-value=1.7e-15  Score=127.48  Aligned_cols=80  Identities=26%  Similarity=0.520  Sum_probs=72.2

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +++||.++++++++++|+++|++||+|.+|.|++++.++.+||||||+|.+.++|++|     +.++++.|.|+.|.|.+
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~a-----l~~~~~~l~G~~i~V~~   95 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA-----MAARPHSIDGRVVEPKR   95 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHH-----HTSCSEEETTEEEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHH-----HHhCCCeECCEEEEEEE
Confidence            4566666666999999999999999999999999999999999999999999999995     56899999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        96 a~~ke  100 (103)
T d1x4ba1          96 AVARE  100 (103)
T ss_dssp             CSSCC
T ss_pred             CcccC
Confidence            88764

>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=99.57  E-value=2.7e-15  Score=120.15  Aligned_cols=76  Identities=30%  Similarity=0.580  Sum_probs=68.3

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +++++.++++++|+++|+++|++||+|..++++.++.+++++|||||+|.++++|++|     +.++++.|.|++|.|+.
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~a-----l~~~~~~l~Gr~i~V~~   77 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI-----VIQKYHTVNGHNCEVRK   77 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH-----HHCSCCEETTEECEEEE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHH-----HHhCCCEECCEEEEEEE
Confidence            4566666666999999999999999999999999999999999999999999988885     57899999999999976


Q ss_pred             h
Q psy15852        180 A  180 (661)
Q Consensus       180 ~  180 (661)
                      |
T Consensus        78 A   78 (79)
T d1l3ka2          78 A   78 (79)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.57  E-value=1.1e-15  Score=123.74  Aligned_cols=78  Identities=27%  Similarity=0.347  Sum_probs=69.9

Q ss_pred             EEEcCCCcCCHHHHHHHhhcCCCeeEE-EEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhh
Q psy15852        103 VSHPGIVHKITEELKEHFSKYGEIENV-TLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAK  181 (661)
Q Consensus       103 ~~~~~~~~~te~~L~~~F~~~G~I~~v-~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~  181 (661)
                      ++.++++++++++|+++|++||+|.++ +|++++.+|+++|||||+|.++++|++|    +..+++..+.|++|.|.++.
T Consensus         2 fV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A----i~~~~g~~~~gr~l~v~~a~   77 (83)
T d1x5ta1           2 FIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA----IEAMNGQYLCNRPITVSYAF   77 (83)
T ss_dssp             EEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHH----HHTTTTCEETTEECEEEESC
T ss_pred             EEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHH----HHhCCCcEECCEEEEEEEec
Confidence            444455599999999999999998764 7899999999999999999999999999    88999999999999999987


Q ss_pred             ccC
Q psy15852        182 AKS  184 (661)
Q Consensus       182 ~~~  184 (661)
                      ++.
T Consensus        78 ~k~   80 (83)
T d1x5ta1          78 KKD   80 (83)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.57  E-value=1.1e-15  Score=123.06  Aligned_cols=78  Identities=12%  Similarity=0.052  Sum_probs=64.2

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      ++++.++++++|+++|+++|++||+|..+.++.+..+|+++|||||+|.++++|++|    +..+|+..+.|++|.|.++
T Consensus         3 tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~A----i~~l~g~~~~g~~i~V~~a   78 (81)
T d2ghpa1           3 TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC----VEKLNGLKIEGYTLVTKVS   78 (81)
T ss_dssp             EEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHH----HHHHTTCEETTEECEEEEC
T ss_pred             EEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHH----HHHhCCCEECCEEEEEEEc
Confidence            445555555999999999999999999999988888899999999999999999999    8899999999999999988


Q ss_pred             hc
Q psy15852        181 KA  182 (661)
Q Consensus       181 ~~  182 (661)
                      +|
T Consensus        79 ~P   80 (81)
T d2ghpa1          79 NP   80 (81)
T ss_dssp             CC
T ss_pred             cC
Confidence            76

>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=99.56  E-value=2.2e-15  Score=122.49  Aligned_cols=77  Identities=27%  Similarity=0.396  Sum_probs=68.6

Q ss_pred             EEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCC---CcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        103 VSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTG---RSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       103 ~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg---~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +|.++++++|+++|+++|++||+|.+|+|++++.++   ++||||||+|.++++|.+|    +..+++..+.|++|.|.+
T Consensus         2 fV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A----~~~~~~~~~~g~~i~V~~   77 (85)
T d2cpfa1           2 FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA----LKQLQGHTVDGHKLEVRI   77 (85)
T ss_dssp             EEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHH----HHHSTTCEETTEECEEEC
T ss_pred             EEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHH----HHHhCCCEECCEEEEEEE
Confidence            445555599999999999999999999999987765   5799999999999999999    889999999999999998


Q ss_pred             hhcc
Q psy15852        180 AKAK  183 (661)
Q Consensus       180 ~~~~  183 (661)
                      +.+.
T Consensus        78 a~~~   81 (85)
T d2cpfa1          78 SERA   81 (85)
T ss_dssp             SSCS
T ss_pred             CCCC
Confidence            8654

>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=99.56  E-value=1.8e-15  Score=123.73  Aligned_cols=78  Identities=26%  Similarity=0.554  Sum_probs=69.8

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      .+++|||+|||+++++++|+++|++||+|.+|+++.     .+++||||+|.+.++|++|+. .++.|+|++|.|.++.+
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCCC
Confidence            457999999999999999999999999999998764     458999999999999999986 56789999999999987


Q ss_pred             CCCC
Q psy15852        263 KPEP  266 (661)
Q Consensus       263 k~~~  266 (661)
                      +...
T Consensus        78 k~~~   81 (88)
T d1wf0a_          78 KHNS   81 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>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=99.56  E-value=3.7e-15  Score=117.79  Aligned_cols=74  Identities=16%  Similarity=0.279  Sum_probs=68.1

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEec
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA  260 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a  260 (661)
                      .+|||+|||+++++++|+++|++||+|..|+++.++..  .++||||+|.++++|++|+..+++.|+|++|.|..+
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--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            47999999999999999999999999999999988753  467999999999999999987789999999999875

>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=99.56  E-value=5.9e-15  Score=124.79  Aligned_cols=84  Identities=17%  Similarity=0.233  Sum_probs=76.4

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      ...+|||+|||+++++++|+++|+++|.|..+.++.+..+++++|||||+|.++++|++|++.+++.|.||.|+|.++.+
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~~~   93 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSR   93 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEECT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEECCH
Confidence            34689999999999999999999999999987777777889999999999999999999998778899999999999988


Q ss_pred             CCCC
Q psy15852        263 KPEP  266 (661)
Q Consensus       263 k~~~  266 (661)
                      ++.+
T Consensus        94 ~~~~   97 (104)
T d1wg5a_          94 AEVR   97 (104)
T ss_dssp             TTSC
T ss_pred             HHhc
Confidence            7543

>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=99.56  E-value=2e-15  Score=135.06  Aligned_cols=81  Identities=25%  Similarity=0.394  Sum_probs=72.8

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      ++++|.+|++++++++|+++|++||+|.+|+|++++.||++||||||+|.+.++|.+|    +..+|+..|.|++|.|.+
T Consensus        43 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~A----i~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA----IAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             SEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHH----HHHTTTEECSSCEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHH----HHHhCCCEECCEEEEEEE
Confidence            3455555555999999999999999999999999999999999999999999999999    889999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus       119 a~~~~  123 (139)
T d1u6fa1         119 AASGH  123 (139)
T ss_dssp             SSCCC
T ss_pred             cCCCC
Confidence            86543

>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=99.56  E-value=2.1e-15  Score=119.53  Aligned_cols=60  Identities=28%  Similarity=0.521  Sum_probs=58.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        595 KMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       595 ~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      +|||+|||+++||+||+++|+.||.|..+.+++++.+|+++|||||+|.+.++|.+|++.
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~   60 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI   60 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhc
Confidence            699999999999999999999999999999999999999999999999999999999974

>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=99.56  E-value=1.4e-15  Score=125.21  Aligned_cols=82  Identities=28%  Similarity=0.495  Sum_probs=74.0

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..+++|.++++++++++|+++|++||+|..|.++.++.++.++|||||+|.++++|++|    +..+++..+.|++|.|.
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A----i~~l~~~~~~g~~l~V~   80 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA----MMAMNGKSVDGRQIRVD   80 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHH----HHHHTTCCTTSCCCEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHH----HHHcCCCEECCEEEEEE
Confidence            35566666666999999999999999999999999999999999999999999999999    88999999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        81 ~a~~~~   86 (90)
T d1x5sa1          81 QAGKSS   86 (90)
T ss_dssp             EEECCC
T ss_pred             EcCCCC
Confidence            987653

>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=99.56  E-value=4e-15  Score=123.65  Aligned_cols=78  Identities=19%  Similarity=0.432  Sum_probs=71.3

Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                      .+..++|||+|||..+++++|+++|++||+|.+|+++++      +|||||+|.+.++|.+|+..+ +..+.|+.|+|.|
T Consensus        15 ~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~   88 (96)
T d1x4ga1          15 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   88 (96)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            455678999999999999999999999999999999865      799999999999999999875 7899999999999


Q ss_pred             ccCCC
Q psy15852        260 ATPKP  264 (661)
Q Consensus       260 a~~k~  264 (661)
                      +++++
T Consensus        89 ak~~p   93 (96)
T d1x4ga1          89 GKESP   93 (96)
T ss_dssp             CCCCC
T ss_pred             cCCCC
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=99.55  E-value=4.1e-15  Score=122.23  Aligned_cols=79  Identities=14%  Similarity=0.181  Sum_probs=68.9

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +++++.++++++++++|+++|++||+|.+|+|++++.+  .+|||||+|.+.++|.+|    +..+++..+.|+.|.|.+
T Consensus         9 ~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A----~~~l~~~~~~g~~i~v~~   82 (90)
T d2cqia1           9 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAA----LAAMNGRKILGKEVKVNW   82 (90)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHH----HHHHTTEEETTEEEEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHH----HHHcCCCEECCEEEEEEE
Confidence            34444445559999999999999999999999998754  489999999999999999    889999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        83 a~~~~   87 (90)
T d2cqia1          83 ATTPS   87 (90)
T ss_dssp             CCCTT
T ss_pred             cCCCC
Confidence            87654

>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=99.55  E-value=4.2e-15  Score=125.17  Aligned_cols=83  Identities=18%  Similarity=0.291  Sum_probs=75.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeE--------EEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCe
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNII--------ETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDK  253 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~--------~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~  253 (661)
                      ..++|||+|||+.+++++|+++|++||.|.        .+.+..++.+++++|||||+|.++++|.+|++.+ +..|+|+
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr   86 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGS   86 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCE
Confidence            457999999999999999999999999884        5677788888999999999999999999999985 7899999


Q ss_pred             EEEEEeccCCCC
Q psy15852        254 EVDVKKATPKPE  265 (661)
Q Consensus       254 ~i~V~~a~~k~~  265 (661)
                      .|.|+++.+++.
T Consensus        87 ~i~V~~a~~~~p   98 (101)
T d2cpea1          87 KLKVSLARKKPP   98 (101)
T ss_dssp             ECEEECSSCCCC
T ss_pred             EEEEEEcCCCCC
Confidence            999999987653

>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=99.54  E-value=8.1e-15  Score=121.71  Aligned_cols=80  Identities=19%  Similarity=0.387  Sum_probs=71.6

Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEe
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKK  259 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~  259 (661)
                      ...+++|||+|||+++++++|+++|++||.|..+.+..+   ..+++||||+|.+.++|++||+.+ +..|.|++|.|.+
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            345678999999999999999999999999999998765   456899999999999999999875 7899999999999


Q ss_pred             ccCC
Q psy15852        260 ATPK  263 (661)
Q Consensus       260 a~~k  263 (661)
                      +++.
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8753

>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=99.54  E-value=3.8e-15  Score=128.36  Aligned_cols=101  Identities=20%  Similarity=0.322  Sum_probs=82.6

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .++|||+|+| ++++++|+++|++||+|.+|++..+   +.++|||||+|.+.++|..|    +..+|+..|.|+.|.|.
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~A----i~~l~g~~~~gr~l~V~   79 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNA----CDHLSGFNVCNRYLVVL   79 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHH----HHHhCCCEECCEEEEEE
Confidence            3455555555 9999999999999999999999875   66899999999999999999    99999999999999998


Q ss_pred             hhhccCCeeEecCCCccCCHHHHHHHHhcCCC
Q psy15852        179 KAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGN  210 (661)
Q Consensus       179 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~  210 (661)
                      ++.+..   ..........+++++.+..+||.
T Consensus        80 ~a~~~~---~~~~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          80 YYNANR---AFQKMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             ECCHHH---HTTTSCHHHHHHHHHHHHHHHCC
T ss_pred             EcCCCc---hhhhhHHHHHHHHHHHHHHHhCC
Confidence            875432   12244555667788888888874

>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=99.54  E-value=4.9e-16  Score=127.91  Aligned_cols=80  Identities=16%  Similarity=0.286  Sum_probs=72.6

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      ...+|||+|||+++++++|+++|++||.|..+.++. ..+|+++|||||+|.+.++|++||+.++..+.|++|.|.++..
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~-~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCE-EEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeee-cCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEecCC
Confidence            346899999999999999999999999999988865 4579999999999999999999998668899999999999986


Q ss_pred             C
Q psy15852        263 K  263 (661)
Q Consensus       263 k  263 (661)
                      |
T Consensus        91 k   91 (91)
T d1fjeb1          91 R   91 (91)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.53  E-value=1.1e-15  Score=129.10  Aligned_cols=84  Identities=17%  Similarity=0.301  Sum_probs=77.9

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ++++|||+|||.++++++|+++|++||.|..+.++.+..+++++|||||+|.+.++|.+|++.+ +..+.|++|.|.|+.
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            4579999999999999999999999999999999888888999999999999999999999987 689999999999999


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      ++.++
T Consensus        97 ~k~~r  101 (102)
T d2cpxa1          97 NKKQR  101 (102)
T ss_dssp             CCSCC
T ss_pred             CcccC
Confidence            87653

>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=99.53  E-value=1e-14  Score=125.68  Aligned_cols=78  Identities=10%  Similarity=0.195  Sum_probs=71.2

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      .+++|||+|||.++++++|+++|++||.|.+|++..+   +.++|||||+|.+.++|.+|++.+ +..|.|+.|.|.++.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3578999999999999999999999999999999865   567999999999999999999876 789999999999987


Q ss_pred             CC
Q psy15852        262 PK  263 (661)
Q Consensus       262 ~k  263 (661)
                      ++
T Consensus        83 ~~   84 (114)
T d2f9da1          83 AN   84 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=99.53  E-value=1.3e-14  Score=119.85  Aligned_cols=79  Identities=22%  Similarity=0.403  Sum_probs=69.9

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+|+|+.++.  .++|||||+|.++++|.+|    +..+++..+.|+.|.|.+
T Consensus        12 ~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~A----i~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1          12 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRA----REKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             CEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHH----HHHHTTCEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHH----HHHcCCCEECCEEEEEEe
Confidence            4455555555999999999999999999999999864  4799999999999999999    889999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        86 A~~r~   90 (93)
T d2cq3a1          86 ATARV   90 (93)
T ss_dssp             CCSSC
T ss_pred             cCcCC
Confidence            98764

>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=99.53  E-value=1.5e-14  Score=122.18  Aligned_cols=68  Identities=24%  Similarity=0.116  Sum_probs=61.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCccc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY  659 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~~  659 (661)
                      ....|||+|||+++||+||+++|+.||.|..+.++++..+++++|||||+|.++++|.+|++...+++
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i   81 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERI   81 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEE
Confidence            35689999999999999999999999999998888888899999999999999999999998554443

>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=99.51  E-value=1.6e-14  Score=121.33  Aligned_cols=65  Identities=18%  Similarity=0.207  Sum_probs=60.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      .++|||+|||+++|+++|+++|++||.|.+++++.+. +++++|||||+|.+.++|.+||+++|..
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~   82 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGK   82 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCC
Confidence            4789999999999999999999999999999999885 6999999999999999999999987654

>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=99.51  E-value=4.3e-15  Score=119.10  Aligned_cols=75  Identities=15%  Similarity=0.390  Sum_probs=66.8

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CC-ccCCeEEEEEeccC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQ-KINDKEVDVKKATP  262 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~-~~~g~~i~V~~a~~  262 (661)
                      ++|||+|||.++++++|+++|++||.|.++.+.      .++|||||+|.+.++|.+|++.+ +. .++|++|.|.++.+
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 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE------EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEe------cccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            479999999999999999999999998776664      35899999999999999999886 44 69999999999998


Q ss_pred             CCC
Q psy15852        263 KPE  265 (661)
Q Consensus       263 k~~  265 (661)
                      +..
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            764

>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=99.51  E-value=6.4e-15  Score=119.89  Aligned_cols=79  Identities=22%  Similarity=0.400  Sum_probs=64.1

Q ss_pred             CcEEEEcCCCcCC-HHHHHHHhhcCCCeeEEEEeeC-CCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852        100 NKMVSHPGIVHKI-TEELKEHFSKYGEIENVTLKSD-PNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus       100 ~~~~~~~~~~~~t-e~~L~~~F~~~G~I~~v~l~~~-~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      +++++.+++++++ +++|+++|++||+|.+|+|+.+ +.+++++|||||+|.+.++|++|    + .+|+..+.|+.|.|
T Consensus         5 ~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~A----l-~~n~~~~~gr~l~V   79 (86)
T d2ghpa3           5 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA----L-QMNRSLLGNREISV   79 (86)
T ss_dssp             TEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHH----G-GGTTEEETTEEEEE
T ss_pred             CEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHH----H-hcCCCEECCEEEEE
Confidence            3444444445775 5669999999999999999764 56789999999999999999997    6 69999999999999


Q ss_pred             hhhhcc
Q psy15852        178 KKAKAK  183 (661)
Q Consensus       178 ~~~~~~  183 (661)
                      .++.++
T Consensus        80 ~~a~~k   85 (86)
T d2ghpa3          80 SLADKK   85 (86)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            998765

>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=99.51  E-value=8.2e-15  Score=120.09  Aligned_cols=79  Identities=20%  Similarity=0.357  Sum_probs=69.4

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .+++|.++++++++++|+++|++||.|.+|+|+.++  +.++|||||+|.+.++|++|    +..+|+..|.|++|.|.+
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~A----i~~l~g~~~~g~~i~V~~   82 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERA----IEKMNGMLLNDRKVFVGR   82 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHH----TTSSSEEEETTEEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHH----HHHcCCCEECCEEEEEEE
Confidence            345555555599999999999999999999999986  45899999999999999998    888999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        83 a~~~~   87 (89)
T d1cvja2          83 FKSRK   87 (89)
T ss_dssp             CCCTT
T ss_pred             CCCCC
Confidence            87654

>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=99.51  E-value=9.2e-15  Score=118.82  Aligned_cols=75  Identities=25%  Similarity=0.450  Sum_probs=69.1

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      .++|||+|||.++++++|+++|++||+|.+|.+.++      ++||||+|.+.++|.+|++.+ +..+.|+.|.|+||..
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            468999999999999999999999999999999754      789999999999999999986 6899999999999987


Q ss_pred             CC
Q psy15852        263 KP  264 (661)
Q Consensus       263 k~  264 (661)
                      +.
T Consensus        82 ~~   83 (86)
T d2cpja1          82 SA   83 (86)
T ss_dssp             CS
T ss_pred             cC
Confidence            54

>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=99.51  E-value=1.7e-14  Score=120.59  Aligned_cols=82  Identities=20%  Similarity=0.339  Sum_probs=72.1

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhC------Ceeecc
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEG------NHVINN  172 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~------~~~i~g  172 (661)
                      ..++++.++++++|+++|+++|++||+|.++.++.++.+++++|||||+|.+.++|.+|    +..++      +..+.|
T Consensus         8 ~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~a----i~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           8 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC----LAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHH----HHHHCTTTTTCCEESSS
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHH----HHHcccccccCCcEECC
Confidence            34566666666999999999999999999999999999999999999999999999999    76664      778999


Q ss_pred             eeehhhhhhccC
Q psy15852        173 KKIEAKKAKAKS  184 (661)
Q Consensus       173 ~~i~v~~~~~~~  184 (661)
                      +.|.|.++.+++
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            999999987654

>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=99.50  E-value=1.7e-14  Score=117.38  Aligned_cols=77  Identities=14%  Similarity=0.306  Sum_probs=69.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      +.++|||+|||+++++++|+++|++||.|..+.+      ++++|||||+|.++++|.+|+..+ +..+.|+.|.|.|+.
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 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE------EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEE------ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            3478999999999999999999999999988877      345899999999999999999986 688999999999998


Q ss_pred             CCCC
Q psy15852        262 PKPE  265 (661)
Q Consensus       262 ~k~~  265 (661)
                      |+..
T Consensus        81 P~~~   84 (86)
T d2cpda1          81 PVDK   84 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.50  E-value=1.2e-14  Score=120.89  Aligned_cols=63  Identities=21%  Similarity=0.249  Sum_probs=58.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcCCC-eeEEEEeecCC-CCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        594 NKMVSHPGIVDKITEELKEHFSKYGE-IENVTLKSDPN-TGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       594 ~~l~v~nlp~~~te~dL~~~F~~~G~-I~~v~i~~d~~-tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      ++|||+|||.++|+++|+++|+.||+ |.+|+|++|.. +|+++|||||+|.++++|.+|+..++
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~   66 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLM   66 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTT
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHc
Confidence            58999999999999999999999996 99999999864 69999999999999999999998764

>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=99.50  E-value=8.7e-15  Score=119.19  Aligned_cols=67  Identities=13%  Similarity=0.100  Sum_probs=59.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCccc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY  659 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~~  659 (661)
                      .+.|||+|||++++++||+++|+.||.|..+.++.+..+|+++|+|||+|.+.++|.+|++++|..+
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~   75 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRP   75 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCE
Confidence            4679999999999999999999999999875445555679999999999999999999999987654

>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=99.50  E-value=1.2e-14  Score=122.24  Aligned_cols=80  Identities=9%  Similarity=0.179  Sum_probs=71.2

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK  263 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k  263 (661)
                      ..+|||+|||+++|++||+++|+.||. ..|.++.+.. +.++|||||+|.+.++|++|++.+++.|+||.|+|.++.++
T Consensus        15 ~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~-g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s~~~   92 (102)
T d1weza_          15 GHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPD-GRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTA   92 (102)
T ss_dssp             SCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSS-SCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEECCC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecC-CcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            468999999999999999999999984 5677777654 88999999999999999999987789999999999998876


Q ss_pred             CC
Q psy15852        264 PE  265 (661)
Q Consensus       264 ~~  265 (661)
                      ..
T Consensus        93 ~~   94 (102)
T d1weza_          93 GT   94 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.49  E-value=1e-14  Score=119.43  Aligned_cols=75  Identities=17%  Similarity=0.341  Sum_probs=67.3

Q ss_pred             CCeeEecCCCccCCHHHH---HHHHhcCCCeEEEEeccCCCCCCc---CcEEEEEeCCHHHHHHHHHhC-CCccCCeEEE
Q psy15852        184 SGKIFVGGLSPEMKDEEI---KAHFAQFGNIIETEMPYDKSKSQR---KNFCFITFEHESVVIDLLKNP-KQKINDKEVD  256 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L---~~~F~~~G~i~~v~i~~~~~~g~~---~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~  256 (661)
                      .++|||+|||+++++++|   +++|++||+|.+|.+++++.++.+   +|||||+|.+.++|.+|++.+ +..++|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            467999999999999999   778999999999999998876554   489999999999999999876 6899999999


Q ss_pred             EE
Q psy15852        257 VK  258 (661)
Q Consensus       257 V~  258 (661)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            84

>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=99.49  E-value=9.1e-15  Score=119.09  Aligned_cols=79  Identities=14%  Similarity=0.118  Sum_probs=69.2

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      +....|||+|||++++++||+++|+.||.|....++.+..+++++|+|||+|.+.++|++|++.+ +..+.|++|+|+++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            44567999999999999999999999999876544444567999999999999999999999986 78999999999875

>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=99.49  E-value=3.1e-14  Score=114.92  Aligned_cols=76  Identities=18%  Similarity=0.262  Sum_probs=68.1

Q ss_pred             hccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCcc-CCeEEEEE
Q psy15852        181 KAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKI-NDKEVDVK  258 (661)
Q Consensus       181 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~-~g~~i~V~  258 (661)
                      .|++++|||+|||.++++++|+++|++||+|..|+++++     .+|||||+|.+.++|.+|++.+ +..+ +|++|.|.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            456789999999999999999999999999999999764     3789999999999999999986 6666 57999999


Q ss_pred             ecc
Q psy15852        259 KAT  261 (661)
Q Consensus       259 ~a~  261 (661)
                      |++
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            986

>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=99.49  E-value=2e-14  Score=120.71  Aligned_cols=77  Identities=17%  Similarity=0.233  Sum_probs=68.6

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      ++++.++++++++++|+++|++||+|..+++..+. +++++|||||+|.+.++|++|    +..+||..|.|+++.|.++
T Consensus        20 ~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~A----i~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          20 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAV----IGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             EEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHH----HHHHBTCCCCCCTTSCCCS
T ss_pred             EEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHH----HHHhCCCEECCcCCccCCC
Confidence            45555555599999999999999999999999875 689999999999999999999    8999999999999999877


Q ss_pred             hc
Q psy15852        181 KA  182 (661)
Q Consensus       181 ~~  182 (661)
                      .|
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.49  E-value=2.5e-14  Score=112.91  Aligned_cols=61  Identities=15%  Similarity=0.117  Sum_probs=55.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        594 NKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       594 ~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      ++|||+|||+++++++|+++|+.||.|.+|+|+.++.  ..+|||||+|.+.++|.+|+....
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~~~~   61 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAITKTH   61 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHTTTT
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHHhcC
Confidence            5799999999999999999999999999999999875  345799999999999999997543

>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=99.49  E-value=1.8e-14  Score=119.80  Aligned_cols=78  Identities=18%  Similarity=0.258  Sum_probs=69.9

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ..++|||+|||+++++++|+++|++||.|..+..     ++.+++||||+|.+.++|.+|++.+ +..|+|++|.|.|+.
T Consensus        15 ~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~   89 (96)
T d1fjca_          15 AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            3478999999999999999999999998876643     4788999999999999999999987 689999999999999


Q ss_pred             CCCC
Q psy15852        262 PKPE  265 (661)
Q Consensus       262 ~k~~  265 (661)
                      ++..
T Consensus        90 ~k~~   93 (96)
T d1fjca_          90 EKGG   93 (96)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            8764

>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=99.49  E-value=3.4e-14  Score=118.32  Aligned_cols=73  Identities=21%  Similarity=0.477  Sum_probs=66.1

Q ss_pred             CCeeEecCCC-ccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        184 SGKIFVGGLS-PEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       184 ~~~lfV~nLp-~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      .++|||+||| ..+++++|+++|++||+|.+|.|        ++|||||+|.+.++|.+||+.+ +..|.|+.|+|.++.
T Consensus        15 ~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   86 (98)
T d1wf2a_          15 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAA   86 (98)
T ss_dssp             CCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETT
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            4689999997 56889999999999999999998        3799999999999999999987 689999999999997


Q ss_pred             CCC
Q psy15852        262 PKP  264 (661)
Q Consensus       262 ~k~  264 (661)
                      ++.
T Consensus        87 ~~~   89 (98)
T d1wf2a_          87 EPK   89 (98)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            653

>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=99.48  E-value=1.5e-14  Score=122.02  Aligned_cols=80  Identities=10%  Similarity=0.056  Sum_probs=71.5

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccCC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK  263 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~k  263 (661)
                      ..+|||+|||+++++++|+++|+.||.|..+.++....+|+++|||||+|.+.++|++||+.++..|+|+.|.|.++..+
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~~~   87 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTLE   87 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEECHH
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECCHH
Confidence            46899999999999999999999999988755555566799999999999999999999987688999999999998654

>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=99.48  E-value=2e-14  Score=118.26  Aligned_cols=79  Identities=20%  Similarity=0.418  Sum_probs=70.3

Q ss_pred             CCeeEecCCCccCCHHHHHH----HHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEE
Q psy15852        184 SGKIFVGGLSPEMKDEEIKA----HFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVK  258 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~----~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~  258 (661)
                      +++|||+|||+.++++||++    +|++||+|.+|.+..   +++++|||||+|.+.++|.+|++.+ +..++|+.|.|.
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            57999999999999998864    689999999999865   3678999999999999999999876 688999999999


Q ss_pred             eccCCCC
Q psy15852        259 KATPKPE  265 (661)
Q Consensus       259 ~a~~k~~  265 (661)
                      |+.++.+
T Consensus        80 ~ak~~~~   86 (91)
T d1nu4a_          80 YAKTDSD   86 (91)
T ss_dssp             ECSSCCT
T ss_pred             EeCCCch
Confidence            9987654

>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=99.48  E-value=1.3e-14  Score=113.77  Aligned_cols=70  Identities=19%  Similarity=0.257  Sum_probs=64.1

Q ss_pred             EEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeeh
Q psy15852        103 VSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIE  176 (661)
Q Consensus       103 ~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~  176 (661)
                      ++.++++++|+++|+++|++||+|.++++++++.++.++|||||+|.++++|++|    +..+|+..+.|+.++
T Consensus         2 yV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A----i~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           2 YIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA----VTALKASGVQAQMAK   71 (72)
T ss_dssp             EEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHH----HHHHHHHTCCEESCC
T ss_pred             EEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHH----HHHhCCCEECCEECc
Confidence            4445555999999999999999999999999999999999999999999999999    889999999998874

>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=99.48  E-value=7.3e-15  Score=119.82  Aligned_cols=73  Identities=15%  Similarity=0.250  Sum_probs=65.8

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      ++|||+|||+.+++++|+++|++||+|.++.+..       .|||||+|.+.++|++||+.+ +..|.|+.|.|.++..+
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 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            4799999999999999999999999999999864       489999999999999999875 78999999998887655


Q ss_pred             C
Q psy15852        264 P  264 (661)
Q Consensus       264 ~  264 (661)
                      .
T Consensus        74 ~   74 (87)
T d3begb1          74 V   74 (87)
T ss_dssp             E
T ss_pred             c
Confidence            4

>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=99.48  E-value=2.6e-14  Score=114.21  Aligned_cols=74  Identities=24%  Similarity=0.440  Sum_probs=66.9

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      +.++|||+||+  +|+++|+++|++||.|.+|.+.+      .++||||+|.+.++|.+|++.+ +..++|++|+|.|+.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET------TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeecc------CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            45799999996  89999999999999999999964      3789999999999999999886 689999999999998


Q ss_pred             CCC
Q psy15852        262 PKP  264 (661)
Q Consensus       262 ~k~  264 (661)
                      +++
T Consensus        76 ~~P   78 (79)
T d2bz2a1          76 KQP   78 (79)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            764

>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=99.48  E-value=2.6e-14  Score=122.37  Aligned_cols=75  Identities=15%  Similarity=0.179  Sum_probs=68.3

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      .++|||+|||+.+++++|+++|++||+|..|.|.      .++|||||+|.+.++|.+|++.+ +..|.|+.|.|.|+..
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            3689999999999999999999999999999884      34899999999999999999886 7899999999999976


Q ss_pred             CC
Q psy15852        263 KP  264 (661)
Q Consensus       263 k~  264 (661)
                      ..
T Consensus        84 ~~   85 (111)
T d1whxa_          84 GV   85 (111)
T ss_dssp             TT
T ss_pred             Cc
Confidence            54

>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=99.48  E-value=2.5e-14  Score=120.33  Aligned_cols=80  Identities=20%  Similarity=0.326  Sum_probs=70.0

Q ss_pred             CcEEEEcCC-CcCCHHHHHHHhhcCCCee--------EEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeee
Q psy15852        100 NKMVSHPGI-VHKITEELKEHFSKYGEIE--------NVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVI  170 (661)
Q Consensus       100 ~~~~~~~~~-~~~te~~L~~~F~~~G~I~--------~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i  170 (661)
                      .+.||++|+ +++++++|+++|++||+|.        .+.+.+++.+|+++|||||+|.++++|.+|    +..+++..|
T Consensus         8 ~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~A----i~~l~g~~~   83 (101)
T d2cpea1           8 NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAA----VEWFDGKDF   83 (101)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHH----HHHHTTCEE
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHH----HHHhCCCEE
Confidence            344555555 5999999999999999874        577888888999999999999999999999    899999999


Q ss_pred             cceeehhhhhhcc
Q psy15852        171 NNKKIEAKKAKAK  183 (661)
Q Consensus       171 ~g~~i~v~~~~~~  183 (661)
                      .|++|.|.+++++
T Consensus        84 ~gr~i~V~~a~~~   96 (101)
T d2cpea1          84 QGSKLKVSLARKK   96 (101)
T ss_dssp             TTEECEEECSSCC
T ss_pred             CCEEEEEEEcCCC
Confidence            9999999998765

>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=99.48  E-value=4.3e-14  Score=115.50  Aligned_cols=78  Identities=12%  Similarity=0.325  Sum_probs=68.3

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCcc-CCeEEEEEe
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKI-NDKEVDVKK  259 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~-~g~~i~V~~  259 (661)
                      |++++|||+|||+++++++|+++|++||.|..+.+..    +++++||||+|.+.++|.+|+..+ +..+ +|+.|+|.+
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 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            5578999999999999999999999999998887765    345889999999999999999876 5666 689999999


Q ss_pred             ccCC
Q psy15852        260 ATPK  263 (661)
Q Consensus       260 a~~k  263 (661)
                      +++.
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            8753

>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=99.46  E-value=4.4e-14  Score=117.25  Aligned_cols=74  Identities=22%  Similarity=0.410  Sum_probs=65.5

Q ss_pred             CcEEEEcCC-CcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGI-VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~-~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .+.|+++++ +++++++|+++|++||+|.+|+|+++      ||||||+|.++++|.+|    +..+++..|.|+.|+|.
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~A----i~~l~~~~i~g~~l~v~   87 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHA----IVSVNGTTIEGHVVKCY   87 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHH----HHHHTTCEETTEECEEE
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHH----HHHhCCCEECCEEEEEE
Confidence            344555555 59999999999999999999999975      68999999999999999    89999999999999999


Q ss_pred             hhhcc
Q psy15852        179 KAKAK  183 (661)
Q Consensus       179 ~~~~~  183 (661)
                      |++++
T Consensus        88 ~ak~~   92 (96)
T d1x4ga1          88 WGKES   92 (96)
T ss_dssp             CCCCC
T ss_pred             EcCCC
Confidence            98764

>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=99.46  E-value=4.5e-14  Score=115.22  Aligned_cols=74  Identities=14%  Similarity=0.207  Sum_probs=64.5

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~  262 (661)
                      +++|||+|||++++++||+++|++|| +..+.+      +.+++||||+|.+.++|++|++.+ +..++|++|.|+++..
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999 333444      456899999999999999999886 6789999999999976


Q ss_pred             CC
Q psy15852        263 KP  264 (661)
Q Consensus       263 k~  264 (661)
                      +.
T Consensus        78 ~~   79 (88)
T d1wg1a_          78 DA   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.46  E-value=3.8e-14  Score=115.94  Aligned_cols=74  Identities=20%  Similarity=0.318  Sum_probs=65.1

Q ss_pred             CcEEEEcCCCcCCHHHH---HHHhhcCCCeeEEEEeeCCCCCCc---ccEEEEEEeehhhHHHhhHHHHHHhCCeeecce
Q psy15852        100 NKMVSHPGIVHKITEEL---KEHFSKYGEIENVTLKSDPNTGRS---RGFAFIVFKDTESLEKASVEDVIAEGNHVINNK  173 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L---~~~F~~~G~I~~v~l~~~~~tg~s---rG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~  173 (661)
                      +++++.++++++++++|   +++|++||+|.+|.|++++.++.+   +|||||+|.++++|.+|    +..+|+..+.|+
T Consensus         9 n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~A----i~~lng~~~~gr   84 (89)
T d2cpia1           9 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRA----IQCVNNVVVDGR   84 (89)
T ss_dssp             SCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHH----HHHHTTEEETTE
T ss_pred             CEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHH----HHHhCCCEECCE
Confidence            45566666669999999   778999999999999999877654   59999999999999999    999999999999


Q ss_pred             eehh
Q psy15852        174 KIEA  177 (661)
Q Consensus       174 ~i~v  177 (661)
                      .|++
T Consensus        85 ~lkv   88 (89)
T d2cpia1          85 TLKA   88 (89)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9976

>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=99.45  E-value=9.5e-14  Score=109.51  Aligned_cols=70  Identities=13%  Similarity=0.314  Sum_probs=62.8

Q ss_pred             eEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       187 lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.++|.+|++.+ +..+.|++|.|+++...
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-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 666665      456999999999999999999876 67999999999999754

>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=99.45  E-value=1e-13  Score=113.24  Aligned_cols=77  Identities=19%  Similarity=0.290  Sum_probs=69.5

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC---CCccCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP---KQKINDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~---~~~~~g~~i~V~  258 (661)
                      +++++|||+|||+++++++|+++|++||.|.++.+.++      ++||||+|.+.++|.+|++.+   +..+.|++|.|.
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            45689999999999999999999999999999998753      689999999999999999863   578999999999


Q ss_pred             eccCCC
Q psy15852        259 KATPKP  264 (661)
Q Consensus       259 ~a~~k~  264 (661)
                      +++.+.
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            998765

>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=99.44  E-value=1e-13  Score=118.13  Aligned_cols=76  Identities=12%  Similarity=0.314  Sum_probs=68.2

Q ss_pred             CCeeEecCCCc-cCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        184 SGKIFVGGLSP-EMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       184 ~~~lfV~nLp~-~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      +++|||+|||+ .+++++|+++|++||+|..|.|++++     +|||||+|.+.++|.+|++.+ +..|.|+.|.|.++.
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 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            36899999965 59999999999999999999998763     789999999999999999886 689999999999987


Q ss_pred             CCC
Q psy15852        262 PKP  264 (661)
Q Consensus       262 ~k~  264 (661)
                      .+.
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

>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=99.44  E-value=4.2e-14  Score=119.25  Aligned_cols=63  Identities=17%  Similarity=0.077  Sum_probs=57.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~  654 (661)
                      ...+|||+|||+++|++||+++|+.||.|..+.++.+..+|+++|||||+|.++++|.+|++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~   69 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL   69 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhc
Confidence            457899999999999999999999999998766666666899999999999999999999974

>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=99.43  E-value=1e-13  Score=116.54  Aligned_cols=62  Identities=19%  Similarity=0.198  Sum_probs=56.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhC
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED  655 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~  655 (661)
                      ...+|||+||||++||+||+++|+.|| |+.|+++++.. |+++|||||+|.+.++|++|++..
T Consensus        14 ~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~-g~~~G~afVeF~~~~~a~~Al~~~   75 (102)
T d1weza_          14 TGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFATHEDAVAAMAKD   75 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSS-SCEEEEEEEECSSSHHHHHHHTTS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecC-CcceEEEEEEECCHHHHHHHHHcC
Confidence            356899999999999999999999997 55899998865 999999999999999999999753

>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=99.43  E-value=3e-13  Score=113.98  Aligned_cols=79  Identities=18%  Similarity=0.193  Sum_probs=70.0

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC---CCccCCeEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP---KQKINDKEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~---~~~~~g~~i~V~  258 (661)
                      +++++|||+|||..+++++|+++|++||.|..+.+.+      .+++|||+|.+.++|++|++.+   ...+.|++|.|.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~------~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~   86 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe------cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEE
Confidence            4567899999999999999999999999999999964      3789999999999999999864   467899999999


Q ss_pred             eccCCCCC
Q psy15852        259 KATPKPEP  266 (661)
Q Consensus       259 ~a~~k~~~  266 (661)
                      ++..+...
T Consensus        87 ~s~~~~~~   94 (104)
T d1wexa_          87 YSTSKRIT   94 (104)
T ss_dssp             ECSSSSCC
T ss_pred             EcCCCccC
Confidence            99876543

>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=99.43  E-value=1.5e-13  Score=113.95  Aligned_cols=77  Identities=21%  Similarity=0.330  Sum_probs=67.0

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .+++|.++++++++++|+++|++||.|..+.+..+   +.++|||||+|.+.++|++|    +..+++..|.|++|.|.+
T Consensus        15 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~A----i~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          15 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDA----VYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHH----HHHHTTCEETTEECEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHH----HHHhCCCEECCEEEEEEe
Confidence            34555555559999999999999999999998764   56799999999999999999    899999999999999999


Q ss_pred             hhcc
Q psy15852        180 AKAK  183 (661)
Q Consensus       180 ~~~~  183 (661)
                      +++.
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8754

>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=99.42  E-value=3.5e-14  Score=115.99  Aligned_cols=59  Identities=29%  Similarity=0.472  Sum_probs=53.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      .++|||+|||+++||+||+++|++||.|.+|+++     ..++|||||+|.+.++|++|+.+.|
T Consensus         5 s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~~~~   63 (88)
T d1wf0a_           5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCGEDL   63 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTTCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHhCCC
Confidence            5799999999999999999999999999999876     3468999999999999999997544

>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=99.42  E-value=1.9e-13  Score=113.66  Aligned_cols=77  Identities=19%  Similarity=0.383  Sum_probs=68.1

Q ss_pred             ccCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCC--eEEEEE
Q psy15852        182 AKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKIND--KEVDVK  258 (661)
Q Consensus       182 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g--~~i~V~  258 (661)
                      ++.++|||+|||+++++++|+++|++||+|..|++.++      ++||||+|.+.++|.+|++.+ +..|.|  ++|+|.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            34589999999999999999999999999999999653      789999999999999999986 567766  689999


Q ss_pred             eccCCC
Q psy15852        259 KATPKP  264 (661)
Q Consensus       259 ~a~~k~  264 (661)
                      |+++.+
T Consensus        89 ~ak~~~   94 (97)
T d1whya_          89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            998654

>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=99.42  E-value=1.2e-14  Score=122.61  Aligned_cols=83  Identities=20%  Similarity=0.205  Sum_probs=73.8

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ++.++++.++++++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|.+|    +..+++..|.|++|.|
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~A----i~~l~g~~~~g~~l~V   92 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQA----LHLVNGYKLYGKILVI   92 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHH----HHHSTTCBCSSCBCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHH----HHHhCCCEECCEEEEE
Confidence            344555555555999999999999999999999998888899999999999999999999    8899999999999999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .+++++.
T Consensus        93 ~~ak~k~   99 (102)
T d2cpxa1          93 EFGKNKK   99 (102)
T ss_dssp             EECCCCS
T ss_pred             EeCCCcc
Confidence            9998754

>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=99.42  E-value=9.4e-15  Score=120.07  Aligned_cols=77  Identities=23%  Similarity=0.266  Sum_probs=67.2

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+++|+.+ .+|++||||||+|.+.++|++|    + ++++..+.|++|.|.+
T Consensus        14 ~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~A----l-~~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          14 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKA----L-ELTGLKVFGNEIKLEK   87 (91)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHH----H-HGGGEEETTEEEEEEC
T ss_pred             cEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHH----H-hcCCcEECCEEEEEEe
Confidence            34555555559999999999999999999998764 5799999999999999999997    6 5999999999999998


Q ss_pred             hhc
Q psy15852        180 AKA  182 (661)
Q Consensus       180 ~~~  182 (661)
                      ++.
T Consensus        88 ak~   90 (91)
T d1fjeb1          88 PKG   90 (91)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            865

>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=99.41  E-value=8e-14  Score=118.51  Aligned_cols=60  Identities=15%  Similarity=0.175  Sum_probs=55.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCC
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV  656 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~  656 (661)
                      ..+|||+|||+++||++|+++|++||.|.+|+|++++    ++|||||+|.++++|++||..++
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln   66 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLD   66 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHH
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHC
Confidence            3579999999999999999999999999999999864    58999999999999999998754

>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=99.41  E-value=9.9e-14  Score=115.48  Aligned_cols=77  Identities=16%  Similarity=0.277  Sum_probs=69.1

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      ...+|||+|||+.+++++|+++|++||+|.+|.+.+       +|||||+|.+.++|++||+.+ +..|.|+.|.|.++.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            346899999999999999999999999999999853       689999999999999999875 689999999999998


Q ss_pred             CCCCC
Q psy15852        262 PKPEP  266 (661)
Q Consensus       262 ~k~~~  266 (661)
                      .+..+
T Consensus        87 ~~~~~   91 (98)
T d1wg4a_          87 VYPER   91 (98)
T ss_dssp             EECCC
T ss_pred             cCCCC
Confidence            76543

>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=99.40  E-value=1.2e-13  Score=118.14  Aligned_cols=66  Identities=14%  Similarity=0.139  Sum_probs=59.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ...+|||+|||+++|++||+++|+.||.|..+.++.+..+|+++|||||+|.+.++|.+|+. +|..
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~   82 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQ   82 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSB
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCC
Confidence            46789999999999999999999999999887777777789999999999999999999996 4443

>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=99.40  E-value=1.2e-13  Score=117.68  Aligned_cols=74  Identities=16%  Similarity=0.249  Sum_probs=65.7

Q ss_pred             cEEEEcCC-C-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        101 KMVSHPGI-V-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       101 ~~~~~~~~-~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ++|+|+|+ | .+++++|+++|++||+|.+|+|++++     +|||||+|.++++|.+|    +..+++..|.|+.|.|.
T Consensus         3 ~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~a----i~~lng~~l~g~~l~v~   73 (109)
T d2adca1           3 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLA----MSHLNGHKLHGKPIRIT   73 (109)
T ss_dssp             SEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHH----HHHHTTCBCSSSBCEEE
T ss_pred             CEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHH----HHHhCCCEECCEEEEEE
Confidence            45666666 6 58999999999999999999999863     68999999999999999    89999999999999999


Q ss_pred             hhhcc
Q psy15852        179 KAKAK  183 (661)
Q Consensus       179 ~~~~~  183 (661)
                      +++..
T Consensus        74 ~s~~~   78 (109)
T d2adca1          74 LSKHQ   78 (109)
T ss_dssp             CCSCC
T ss_pred             ECCCC
Confidence            98644

>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=99.40  E-value=4e-14  Score=121.19  Aligned_cols=81  Identities=16%  Similarity=0.206  Sum_probs=72.6

Q ss_pred             cCCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEeccC
Q psy15852        183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP  262 (661)
Q Consensus       183 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~~  262 (661)
                      ...+|||+|||+++|+++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|++|++.++..|+|+.|.|.++.+
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~~   96 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITK   96 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEECH
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcCh
Confidence            34689999999999999999999999998876666666779999999999999999999998778899999999998865


Q ss_pred             C
Q psy15852        263 K  263 (661)
Q Consensus       263 k  263 (661)
                      +
T Consensus        97 ~   97 (112)
T d1wela1          97 K   97 (112)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.39  E-value=1.9e-13  Score=115.33  Aligned_cols=80  Identities=25%  Similarity=0.361  Sum_probs=66.9

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCC-CCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDP-NTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~-~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ..+++|.++++++++++|+++|++|| |.+++++.++ .+++++|||||+|.+.++|++     ++.+++..|.|+.|.|
T Consensus        15 ~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~-----~~~~~~~~~~gr~l~V   88 (104)
T d1wi8a_          15 PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLS-----ALSLNEESLGNKRIRV   88 (104)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHH-----HHGGGTCEETTEECEE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHH-----HHHcCCCEECCEEEEE
Confidence            34555555555999999999999999 7788887765 468899999999999999976     5689999999999999


Q ss_pred             hhhhccC
Q psy15852        178 KKAKAKS  184 (661)
Q Consensus       178 ~~~~~~~  184 (661)
                      .++.++.
T Consensus        89 ~~a~~~~   95 (104)
T d1wi8a_          89 DVADQAQ   95 (104)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9887643

>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=99.39  E-value=2e-13  Score=116.01  Aligned_cols=78  Identities=10%  Similarity=0.086  Sum_probs=68.6

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCcc--CCeEEEEEec
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKI--NDKEVDVKKA  260 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~--~g~~i~V~~a  260 (661)
                      ..+|||+|||+.+|+++|+++|++||.|..|.++.++    ++|||||+|.+.++|++|++.+ +..|  .++.|.|.++
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s   82 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS   82 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEec
Confidence            3579999999999999999999999999999998753    4899999999999999999987 5555  6789999998


Q ss_pred             cCCCC
Q psy15852        261 TPKPE  265 (661)
Q Consensus       261 ~~k~~  265 (661)
                      .++..
T Consensus        83 ~~~~~   87 (108)
T d2adba1          83 KLTSL   87 (108)
T ss_dssp             SSCSC
T ss_pred             CCccc
Confidence            77553

>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=99.39  E-value=2.5e-13  Score=110.35  Aligned_cols=75  Identities=20%  Similarity=0.261  Sum_probs=64.5

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      +++++.++++++++++|+++|++||.|..+.+.+      ++|||||+|.++++|.+|    +..+++..|.|+.|.|.+
T Consensus         9 k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~A----i~~l~~~~i~g~~i~V~~   78 (86)
T d2cpda1           9 KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEA----MKALNGKVLDGSPIEVTL   78 (86)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHH----HHHHSSEEETTEEEEEEC
T ss_pred             CEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHH----HHHcCCCEECCEEEEEEe
Confidence            3444444555999999999999999998877643      578999999999999999    899999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      ++|+.
T Consensus        79 akP~~   83 (86)
T d2cpda1          79 AKPVD   83 (86)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            98765

>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=99.39  E-value=1.7e-13  Score=109.39  Aligned_cols=75  Identities=20%  Similarity=0.348  Sum_probs=66.3

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      +.++||+++++ +|+++|+++|++||+|.+|++.++      +|||||+|.+.++|.+|    +..+|+..+.|++|.|.
T Consensus         4 ~~~ti~V~~~~-~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~A----i~~lng~~~~g~~l~V~   72 (79)
T d2bz2a1           4 KGNTLYVYGED-MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQA----VAELNGTQVESVQLKVN   72 (79)
T ss_dssp             CCCEEEEECSS-CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHH----HHHHTTCBCSSCBCEEE
T ss_pred             CCCEEEEECCC-CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHH----HHHhCCCEECCEEEEEE
Confidence            44566777765 999999999999999999999764      57999999999999999    99999999999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++++++
T Consensus        73 ~a~~~P   78 (79)
T d2bz2a1          73 IARKQP   78 (79)
T ss_dssp             ECCSSC
T ss_pred             EecCCC
Confidence            997653

>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=99.39  E-value=2.1e-13  Score=113.51  Aligned_cols=73  Identities=21%  Similarity=0.366  Sum_probs=63.5

Q ss_pred             CCcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehh
Q psy15852         99 KNKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEA  177 (661)
Q Consensus        99 ~~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v  177 (661)
                      ..+|+|.+|++ .+++++|+++|++||+|.+|+|        +||||||+|.+.++|++|    +..+|+..|.|++|.|
T Consensus        15 ~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~A----i~~lng~~~~g~~l~V   82 (98)
T d1wf2a_          15 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAA----VAGEDGRMIAGQVLDI   82 (98)
T ss_dssp             CCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHH----HHTTTTCEETTEECEE
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHH----HHHcCCCEECCEEEEE
Confidence            34555555555 6788999999999999999998        368999999999999999    9999999999999999


Q ss_pred             hhhhcc
Q psy15852        178 KKAKAK  183 (661)
Q Consensus       178 ~~~~~~  183 (661)
                      .++.++
T Consensus        83 ~~a~~~   88 (98)
T d1wf2a_          83 NLAAEP   88 (98)
T ss_dssp             EETTSC
T ss_pred             EECCCC
Confidence            998754

>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=99.38  E-value=5.6e-13  Score=110.82  Aligned_cols=58  Identities=14%  Similarity=0.177  Sum_probs=53.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCc
Q psy15852        593 KNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVY  657 (661)
Q Consensus       593 ~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~  657 (661)
                      ..+|||.|||++++++||+++|+.||.|++|+|.+       +|||||+|.+.++|.+||+++|.
T Consensus        15 ~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng   72 (98)
T d1wg4a_          15 DFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDD   72 (98)
T ss_dssp             SCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCC
Confidence            56899999999999999999999999999999974       58999999999999999998664

>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=99.38  E-value=1.6e-13  Score=111.75  Aligned_cols=72  Identities=19%  Similarity=0.222  Sum_probs=64.6

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      ++++|.++++++++++|+++|++||+|.+|+|+++       |||||+|.+.++|++|    +..+++..|.|+.|.|.+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~A----i~~l~g~~~~g~~i~v~~   69 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYA----VRKLDNTKFRSHEGETAY   69 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHH----HHHHTTCBCCCTTSCCCB
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHH----HHHhCCCEECCcEeEEeE
Confidence            46777777779999999999999999999998764       7999999999999999    889999999999999877


Q ss_pred             hhc
Q psy15852        180 AKA  182 (661)
Q Consensus       180 ~~~  182 (661)
                      +.+
T Consensus        70 ~~~   72 (87)
T d3begb1          70 IRV   72 (87)
T ss_dssp             CEE
T ss_pred             Eec
Confidence            643

>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=99.37  E-value=1.9e-13  Score=116.83  Aligned_cols=74  Identities=16%  Similarity=0.203  Sum_probs=64.8

Q ss_pred             CcEEEEcCCC-cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852        100 NKMVSHPGIV-HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~-~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      .++|||+|+| ++++++|+++|++||+|.+|.|..      ++|||||+|.+.++|.+|    +..||+..|.|+.|.|.
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A----~~~lng~~~~gr~l~v~   79 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKA----FRHLAYSKFHHVPLYLE   79 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHH----HHHHTTCBSSSSBCEEE
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHH----HHHHcCCccCCCeEEEE
Confidence            3566666665 999999999999999999998853      578999999999999999    99999999999999998


Q ss_pred             hhhcc
Q psy15852        179 KAKAK  183 (661)
Q Consensus       179 ~~~~~  183 (661)
                      ++...
T Consensus        80 ~a~~~   84 (111)
T d1whxa_          80 WAPIG   84 (111)
T ss_dssp             EEETT
T ss_pred             ECCCC
Confidence            87543

>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=99.37  E-value=2e-13  Score=112.11  Aligned_cols=79  Identities=24%  Similarity=0.359  Sum_probs=67.5

Q ss_pred             CCcEEEEcCCCcCCHHHHHH----HhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeeccee
Q psy15852         99 KNKMVSHPGIVHKITEELKE----HFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK  174 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~----~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~  174 (661)
                      ++++++.+++++++++||++    +|++||+|.+|++.+   +++++|||||+|.+.++|.+|    +..+++..+.|+.
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A----~~~~~~~~~~g~~   75 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA----LRSMQGFPFYDKP   75 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHH----HHHHTTCEETTEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHH----HHHhCCCEECCEE
Confidence            45555555556999999864    689999999998865   477999999999999999999    8899999999999


Q ss_pred             ehhhhhhccC
Q psy15852        175 IEAKKAKAKS  184 (661)
Q Consensus       175 i~v~~~~~~~  184 (661)
                      |.|.++++++
T Consensus        76 l~v~~ak~~~   85 (91)
T d1nu4a_          76 MRIQYAKTDS   85 (91)
T ss_dssp             CEEEECSSCC
T ss_pred             EEEEEeCCCc
Confidence            9999988654

>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=99.36  E-value=4.3e-13  Score=108.08  Aligned_cols=75  Identities=16%  Similarity=0.121  Sum_probs=63.1

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeee-cceeeh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVI-NNKKIE  176 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i-~g~~i~  176 (661)
                      +.+++++.++++++++++|+++|++||+|.+|+++++     .+|||||+|.+.++|.+|    +..+++..+ .|++|.
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A----~~~l~g~~~~~~~~i~   77 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAA----KEALQGFKITPTHAMK   77 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHH----HHHHTTCBSSTTCBCE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHH----HHHhCCcEeCCCcEEE
Confidence            3444555555559999999999999999999999864     368999999999999999    899999888 468899


Q ss_pred             hhhhh
Q psy15852        177 AKKAK  181 (661)
Q Consensus       177 v~~~~  181 (661)
                      |.|++
T Consensus        78 v~~ak   82 (83)
T d2b0ga1          78 ITFAK   82 (83)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            98875

>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=99.36  E-value=3.7e-13  Score=109.16  Aligned_cols=75  Identities=23%  Similarity=0.349  Sum_probs=65.7

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      .++++.++++++++++|+++|++||+|.+|++.++      +|||||+|.+.++|++|    +..+|+..|.|++|.|.+
T Consensus         9 ~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A----~~~l~g~~i~g~~l~V~~   78 (86)
T d2cpja1           9 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIA----KVELDNMPLRGKQLRVRF   78 (86)
T ss_dssp             TEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHH----HHHHTTCCBTTBCCEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHH----HHHhCCCEECCEEEEEEE
Confidence            34555555559999999999999999999999865      57999999999999999    999999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.+..
T Consensus        79 A~~~~   83 (86)
T d2cpja1          79 ACHSA   83 (86)
T ss_dssp             SSCCS
T ss_pred             CCCcC
Confidence            87643

>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=99.36  E-value=4.9e-13  Score=109.06  Aligned_cols=78  Identities=21%  Similarity=0.167  Sum_probs=65.2

Q ss_pred             cCCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeee-cceee
Q psy15852         97 EAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVI-NNKKI  175 (661)
Q Consensus        97 ~~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i-~g~~i  175 (661)
                      ++.+++++.++++++++++|+++|++||.|.++.+..    ++++|||||+|.+.++|.+|    +..+++..+ .|++|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A----~~~l~~~~i~~g~~l   79 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQA----LIDLHNHDLGENHHL   79 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHH----HHHHTTCBSSSSCBC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHH----HHhccCCEecCCCEE
Confidence            3455555555555999999999999999998887765    34688999999999999999    889999888 58999


Q ss_pred             hhhhhhc
Q psy15852        176 EAKKAKA  182 (661)
Q Consensus       176 ~v~~~~~  182 (661)
                      .|.++++
T Consensus        80 ~v~~sk~   86 (88)
T d2adca2          80 RVSFSKS   86 (88)
T ss_dssp             EEEECSS
T ss_pred             EEEeCCC
Confidence            9998865

>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=99.36  E-value=5.6e-13  Score=108.69  Aligned_cols=77  Identities=12%  Similarity=0.041  Sum_probs=68.0

Q ss_pred             ccCCeeEecCCCcc-CCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC---CCccCCeEEEE
Q psy15852        182 AKSGKIFVGGLSPE-MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP---KQKINDKEVDV  257 (661)
Q Consensus       182 ~~~~~lfV~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~---~~~~~g~~i~V  257 (661)
                      ..++.|||+|||.. +|++||.++|++||.|.+|.++.+      +++|||+|++.++|.+|++.+   +..+.|++|.|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            34678999999986 889999999999999999999764      678999999999999999864   56899999999


Q ss_pred             EeccCCC
Q psy15852        258 KKATPKP  264 (661)
Q Consensus       258 ~~a~~k~  264 (661)
                      .|+....
T Consensus        80 ~~s~~~~   86 (89)
T d1x4da1          80 HLSQKYK   86 (89)
T ss_dssp             EEECCCT
T ss_pred             EECCCcc
Confidence            9997543

>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=99.36  E-value=1.7e-13  Score=109.62  Aligned_cols=75  Identities=16%  Similarity=0.169  Sum_probs=65.0

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCe-eecceeehhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH-VINNKKIEAK  178 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~-~i~g~~i~v~  178 (661)
                      +++++.++++++++++|+++|++||.|.++++..      +||||||+|.++++|.+|    +..+|+. .+.|++|.|.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~A----i~~lng~~~~~G~~i~V~   71 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRA----IETLSGKVELHGKIMEVD   71 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHH----HHHHTTTCEETTEECEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHH----HHHhCCCeEECCEEEEEE
Confidence            4566666666999999999999999988777665      478999999999999999    8899985 6999999999


Q ss_pred             hhhccC
Q psy15852        179 KAKAKS  184 (661)
Q Consensus       179 ~~~~~~  184 (661)
                      ++.++.
T Consensus        72 ~a~~k~   77 (80)
T d2cqha1          72 YSVSKK   77 (80)
T ss_dssp             ECCCCC
T ss_pred             EcCCcC
Confidence            998764

>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=99.34  E-value=5e-13  Score=111.41  Aligned_cols=76  Identities=14%  Similarity=0.159  Sum_probs=67.5

Q ss_pred             cCCeeEecCCCcc-CCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHh---CCCccCCeEEEEE
Q psy15852        183 KSGKIFVGGLSPE-MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN---PKQKINDKEVDVK  258 (661)
Q Consensus       183 ~~~~lfV~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~---~~~~~~g~~i~V~  258 (661)
                      ..++|||+|||.+ +|+++|.++|++||.|.++.++++      +|+|||+|.+.++|.+|++.   .+..++|+.|.|.
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~   90 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   90 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEE
Confidence            3578999999985 899999999999999999999754      78999999999999999973   4678999999999


Q ss_pred             eccCCC
Q psy15852        259 KATPKP  264 (661)
Q Consensus       259 ~a~~k~  264 (661)
                      +++.+.
T Consensus        91 ~s~~~~   96 (99)
T d1x4fa1          91 LSEKYK   96 (99)
T ss_dssp             EECSCS
T ss_pred             EcCCcc
Confidence            997654

>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=99.34  E-value=4.1e-13  Score=111.44  Aligned_cols=76  Identities=25%  Similarity=0.353  Sum_probs=64.8

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhh
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK  179 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~  179 (661)
                      ++|++.++++++++++|+++|++||+|..++     .+++++|||||+|.+.++|++|    +..+++..|.|++|.|.+
T Consensus        17 ~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A----~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          17 RTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKN----LEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             GEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHH----HHHTTEEEETTEEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHH----HHHcCCCEECCEEEEEEE
Confidence            3444444445999999999999999886654     2578999999999999999999    889999999999999999


Q ss_pred             hhccC
Q psy15852        180 AKAKS  184 (661)
Q Consensus       180 ~~~~~  184 (661)
                      +.++.
T Consensus        88 a~~k~   92 (96)
T d1fjca_          88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             eCCCC
Confidence            88764

>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=99.33  E-value=2e-14  Score=118.03  Aligned_cols=78  Identities=13%  Similarity=0.236  Sum_probs=67.6

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEecc-----CCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEe
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPY-----DKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKK  259 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~  259 (661)
                      ++|||+|||+++++++|+++|++||.|..+.+..     +..+++++|||||+|.+.++|++|++.++..+.|+.|+|++
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~r   81 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR   81 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCBC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEECC
Confidence            5899999999999999999999999887766543     34567889999999999999999997668999999999975


Q ss_pred             ccC
Q psy15852        260 ATP  262 (661)
Q Consensus       260 a~~  262 (661)
                      ++.
T Consensus        82 ~k~   84 (90)
T d1u2fa_          82 PHD   84 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            443

>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=99.30  E-value=2.2e-12  Score=101.51  Aligned_cols=70  Identities=13%  Similarity=0.212  Sum_probs=59.7

Q ss_pred             EEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhhc
Q psy15852        103 VSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKA  182 (661)
Q Consensus       103 ~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~~  182 (661)
                      +|.++|+++++++|+++|++|| +..+++      ++++|||||+|.+.++|++|    +..+|+..+.|++|.|.++..
T Consensus         2 ~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~A----i~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           2 LIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAA----INTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHH----HHHHTTEESSSCEEEEEECCS
T ss_pred             EEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHH----HHHhCCccCCCCEEEEEEeCC
Confidence            4455555999999999999999 545544      45789999999999999999    999999999999999999865


Q ss_pred             c
Q psy15852        183 K  183 (661)
Q Consensus       183 ~  183 (661)
                      .
T Consensus        71 d   71 (75)
T d1wi6a1          71 D   71 (75)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.27  E-value=1.2e-12  Score=106.49  Aligned_cols=74  Identities=11%  Similarity=0.145  Sum_probs=61.5

Q ss_pred             CCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhh
Q psy15852         99 KNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK  178 (661)
Q Consensus        99 ~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~  178 (661)
                      ..+++|.+++++++++||+++|++||. ..+.+      ++++|||||+|.++++|++|    +..+|+..+.|++|.|.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~------~~~kg~afV~f~~~~~A~~A----i~~ln~~~~~G~~l~V~   73 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV------DRNKRTAFVTLLNGEQAQNA----IQMFHQYSFRGKDLIVQ   73 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE------EGGGTEEEECCSCHHHHHHH----HHHHTTEEETTEEEEEE
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcCc-eeeee------eccCCceEEEECCHHHHHHH----HHHhCCCEECCEEEEEE
Confidence            345666666669999999999999993 23333      45789999999999999999    99999999999999999


Q ss_pred             hhhcc
Q psy15852        179 KAKAK  183 (661)
Q Consensus       179 ~~~~~  183 (661)
                      ++..+
T Consensus        74 ~a~~~   78 (88)
T d1wg1a_          74 LQPTD   78 (88)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            88654

>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=99.26  E-value=4.3e-12  Score=105.30  Aligned_cols=77  Identities=13%  Similarity=0.251  Sum_probs=66.6

Q ss_pred             cCCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecc--ee
Q psy15852         97 EAKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN--KK  174 (661)
Q Consensus        97 ~~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g--~~  174 (661)
                      .+.++|++.++++++++++|+++|++||+|..|++.++      ++||||+|.+.++|++|    +..+++..|.|  ++
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A----~~~l~~~~i~g~~~~   84 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAA----CAKMRGFPLGGPDRR   84 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHH----HHHHTTCBCSSSSCB
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHH----HHHhCCCEeCCCceE
Confidence            34567777777779999999999999999999999864      56999999999999999    99999999976  47


Q ss_pred             ehhhhhhcc
Q psy15852        175 IEAKKAKAK  183 (661)
Q Consensus       175 i~v~~~~~~  183 (661)
                      |.|.++++.
T Consensus        85 l~v~~ak~~   93 (97)
T d1whya_          85 LRVDFAKSG   93 (97)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEeCCCC
Confidence            888888754

>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=99.26  E-value=1.7e-13  Score=112.36  Aligned_cols=64  Identities=13%  Similarity=0.155  Sum_probs=56.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEe-----ecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        594 NKMVSHPGIVDKITEELKEHFSKYGEIENVTLK-----SDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       594 ~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~-----~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ++|||+|||+++||+||+++|+.||.|.++.+.     .+..+++++|||||+|.+.++|++|++ ++.+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~   70 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGI   70 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCc
Confidence            589999999999999999999999999887775     456789999999999999999999986 5443

>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=99.26  E-value=6e-12  Score=105.83  Aligned_cols=58  Identities=16%  Similarity=0.184  Sum_probs=53.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhC
Q psy15852        592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED  655 (661)
Q Consensus       592 ~~~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~  655 (661)
                      ..++|||+|||+++||+||+++|++||.|.+|++.+      .||+|||+|.+.++|++|+..+
T Consensus        14 ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~------~k~~AfV~f~~~e~A~~ai~~~   71 (104)
T d1wexa_          14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFENIDSAKECVTFA   71 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe------cceeEEEEeCCHHHHHHHHHHH
Confidence            357899999999999999999999999999999975      3679999999999999999854

>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=99.25  E-value=7.4e-12  Score=104.93  Aligned_cols=77  Identities=12%  Similarity=0.046  Sum_probs=67.6

Q ss_pred             cCCeeEecCCCccC-CH----HHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEE
Q psy15852        183 KSGKIFVGGLSPEM-KD----EEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVD  256 (661)
Q Consensus       183 ~~~~lfV~nLp~~~-te----~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~  256 (661)
                      ..++|||+||+.++ ++    ++|+++|++||.|.++.+++      +++||||+|.+.++|.+|++.+ +..|+|+.|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            45789999999986 33    57999999999999999964      4789999999999999999998 6899999999


Q ss_pred             EEeccCCCC
Q psy15852        257 VKKATPKPE  265 (661)
Q Consensus       257 V~~a~~k~~  265 (661)
                      |.|+.++..
T Consensus        78 v~~a~~~~~   86 (104)
T d1weya_          78 LYFAQTLHI   86 (104)
T ss_dssp             EECCCCSSC
T ss_pred             EeecccCCC
Confidence            999987654

>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=99.23  E-value=3.5e-12  Score=106.99  Aligned_cols=66  Identities=29%  Similarity=0.388  Sum_probs=61.6

Q ss_pred             cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        110 HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       110 ~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      +++|++|+++|++||+|.+|+|+++ .+++++|||||+|.+.++|.+|    +..+|+..+.|++|.|.+.
T Consensus        38 ~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~A----i~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          38 EFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKA----VIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHH----HHHHTTCEETTEECCEEEC
T ss_pred             hhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHH----HHHHCCCEECCEEEEEEEC
Confidence            7899999999999999999999987 4699999999999999999999    9999999999999988653

>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=99.22  E-value=1.2e-12  Score=109.83  Aligned_cols=75  Identities=9%  Similarity=0.126  Sum_probs=68.7

Q ss_pred             CeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEec
Q psy15852        185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKA  260 (661)
Q Consensus       185 ~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a  260 (661)
                      ..++|++++.++++++|+++|++||+|.+|.|+++ .+++++|||||+|.+.++|.+|++.+ +..++||+|.|.+.
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            35778899999999999999999999999999876 46999999999999999999999986 78999999999875

>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=99.21  E-value=1.4e-11  Score=100.19  Aligned_cols=77  Identities=13%  Similarity=0.097  Sum_probs=63.8

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHH--HhCCeeecceee
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVI--AEGNHVINNKKI  175 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~--~~~~~~i~g~~i  175 (661)
                      +.+++++.++++++++++|+++|++||.|.+|++.++      +|||||+|.+.++|++|    +.  .+++..+.|++|
T Consensus         7 Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a----~~~~~~~~~~~~g~~l   76 (88)
T d2cq1a1           7 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITM----VNYYSAVTPHLRNQPI   76 (88)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHH----HHHHHHSCCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHH----HHHHccCCCccCCCEE
Confidence            4445555555559999999999999999999999864      46999999999999998    55  457889999999


Q ss_pred             hhhhhhccC
Q psy15852        176 EAKKAKAKS  184 (661)
Q Consensus       176 ~v~~~~~~~  184 (661)
                      .|.+++.+.
T Consensus        77 ~v~~sk~~~   85 (88)
T d2cq1a1          77 YIQYSNHKE   85 (88)
T ss_dssp             EEEECSCSS
T ss_pred             EEEECCCCC
Confidence            999887543

>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=99.20  E-value=8.4e-12  Score=104.05  Aligned_cols=62  Identities=16%  Similarity=0.156  Sum_probs=55.4

Q ss_pred             cCCCeEEEcC--CCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhCCcc
Q psy15852        591 EAKNKMVSHP--GIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF  658 (661)
Q Consensus       591 ~~~~~l~v~n--lp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~~~~~~  658 (661)
                      ++.++|||.|  ||+++||++|+++|++||.|..|+++.+      +|||||+|.+.++|.+|+..+|..
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~   79 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGK   79 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTC
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCC
Confidence            3467899966  9999999999999999999999998864      569999999999999999998854

>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=99.19  E-value=9.5e-12  Score=101.25  Aligned_cols=74  Identities=18%  Similarity=0.209  Sum_probs=63.5

Q ss_pred             CCcEEEEcCCC--cCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHH--HhCCeeeccee
Q psy15852         99 KNKMVSHPGIV--HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVI--AEGNHVINNKK  174 (661)
Q Consensus        99 ~~~~~~~~~~~--~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~--~~~~~~i~g~~  174 (661)
                      ..++++++|+|  .+|++||.++|++||+|.+|.+++++      ++|||+|.+.++|..|    +.  ..++..+.|++
T Consensus         7 ~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A----~~~l~~~~~~~~gr~   76 (89)
T d1x4da1           7 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAA----VDYYTTTPALVFGKP   76 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHH----HHHHHHSCCEETTEE
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHH----HHHHhhCCCccCCce
Confidence            45667777777  47899999999999999999998754      4899999999999998    65  44788999999


Q ss_pred             ehhhhhhc
Q psy15852        175 IEAKKAKA  182 (661)
Q Consensus       175 i~v~~~~~  182 (661)
                      |.|.++..
T Consensus        77 l~V~~s~~   84 (89)
T d1x4da1          77 VRVHLSQK   84 (89)
T ss_dssp             CEEEEECC
T ss_pred             EEEEECCC
Confidence            99999864

>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=99.17  E-value=3e-11  Score=95.99  Aligned_cols=73  Identities=21%  Similarity=0.296  Sum_probs=62.7

Q ss_pred             CCeeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeE-EEEEeccC
Q psy15852        184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKE-VDVKKATP  262 (661)
Q Consensus       184 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~-i~V~~a~~  262 (661)
                      ++.|+|.++|++.+++.| ++|++||+|.++++.      +.++||||+|.++++|++||+.++..++|+. |.|+++..
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCCC
Confidence            357999999999987655 579999999999884      4589999999999999999987789999974 67998876


Q ss_pred             C
Q psy15852        263 K  263 (661)
Q Consensus       263 k  263 (661)
                      +
T Consensus        77 k   77 (81)
T d1wwha1          77 K   77 (81)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.16  E-value=1.6e-11  Score=104.65  Aligned_cols=57  Identities=19%  Similarity=0.138  Sum_probs=51.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCH-HHHHHHHHhCCc
Q psy15852        595 KMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDT-ESLEKASVEDVY  657 (661)
Q Consensus       595 ~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~-e~A~~A~~~~~~  657 (661)
                      .+||+|||+++|+++|+++|++||+|.+|+|+++      +|||||.|.++ ++|.+|+..++.
T Consensus        13 ~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~   70 (113)
T d1owxa_          13 LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANN   70 (113)
T ss_dssp             EEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTT
T ss_pred             EEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcC
Confidence            4599999999999999999999999999999953      68999999996 678899987764

>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=99.15  E-value=1.3e-11  Score=102.71  Aligned_cols=75  Identities=13%  Similarity=0.148  Sum_probs=64.3

Q ss_pred             CCcEEEEcCCC-c-CCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHH--HhCCeeeccee
Q psy15852         99 KNKMVSHPGIV-H-KITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVI--AEGNHVINNKK  174 (661)
Q Consensus        99 ~~~~~~~~~~~-~-~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~--~~~~~~i~g~~  174 (661)
                      ..++++++|+| + +|+++|.++|++||+|.+|+++++      +|||||+|.+.++|.+|    +.  .+++..+.|+.
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~A----i~~~~~~~~~~~gr~   86 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAM----VDHCLKKALWFQGRC   86 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHH----HHHHHHSCCCSSSSC
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHH----HHHHhcCCceECCEE
Confidence            34667777776 4 899999999999999999999864      57999999999999998    64  67889999999


Q ss_pred             ehhhhhhcc
Q psy15852        175 IEAKKAKAK  183 (661)
Q Consensus       175 i~v~~~~~~  183 (661)
                      |.|.++..+
T Consensus        87 l~V~~s~~~   95 (99)
T d1x4fa1          87 VKVDLSEKY   95 (99)
T ss_dssp             CEEEEECSC
T ss_pred             EEEEEcCCc
Confidence            999988654

>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=99.14  E-value=2.6e-11  Score=101.58  Aligned_cols=75  Identities=12%  Similarity=0.043  Sum_probs=62.5

Q ss_pred             CcEEEEcCCCcC-----CHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeeccee
Q psy15852        100 NKMVSHPGIVHK-----ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK  174 (661)
Q Consensus       100 ~~~~~~~~~~~~-----te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~  174 (661)
                      .+||+.++.+++     ++++|+++|++||+|.+|++++      ++|||||+|.+.++|.+|    +..+|+..|.|++
T Consensus         6 ~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~A----i~~lng~~~~g~~   75 (104)
T d1weya_           6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADA----RLRLHKTEFLGKE   75 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHH----HHTSTTSEETTEE
T ss_pred             ceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHH----HHHhcccccCCCE
Confidence            445555555443     3467999999999999999985      467999999999999999    9999999999999


Q ss_pred             ehhhhhhccC
Q psy15852        175 IEAKKAKAKS  184 (661)
Q Consensus       175 i~v~~~~~~~  184 (661)
                      |.|.++++..
T Consensus        76 l~v~~a~~~~   85 (104)
T d1weya_          76 MKLYFAQTLH   85 (104)
T ss_dssp             CEEECCCCSS
T ss_pred             eEEeecccCC
Confidence            9999987543

>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=99.11  E-value=3.2e-11  Score=102.83  Aligned_cols=72  Identities=15%  Similarity=0.217  Sum_probs=59.7

Q ss_pred             eeEecCCCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCH-HHHHHHHHhC-CCccCCeEEEEEeccCC
Q psy15852        186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE-SVVIDLLKNP-KQKINDKEVDVKKATPK  263 (661)
Q Consensus       186 ~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~-~~A~~Al~~~-~~~~~g~~i~V~~a~~k  263 (661)
                      .+||+|||+.+|+++|+++|++||+|.+|.|+++      +|||||+|.++ ++|.+|+..+ +..+.++.+.|.++..+
T Consensus        13 ~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~   86 (113)
T d1owxa_          13 LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   86 (113)
T ss_dssp             EEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             EEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeecc
Confidence            4699999999999999999999999999999854      79999999985 7788888887 45566666666665543

>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=99.08  E-value=8.4e-11  Score=97.83  Aligned_cols=64  Identities=11%  Similarity=0.195  Sum_probs=55.6

Q ss_pred             hccCCeeEecC--CCccCCHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCcc
Q psy15852        181 KAKSGKIFVGG--LSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKI  250 (661)
Q Consensus       181 ~~~~~~lfV~n--Lp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~  250 (661)
                      ..+.++|+|.|  ||..+|+++|+++|++||.|..|.++.+      ++||||+|.+.++|.+|++.+ +..+
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            34457888855  9999999999999999999999998754      689999999999999999997 4544

>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=99.03  E-value=2.8e-10  Score=94.31  Aligned_cols=78  Identities=6%  Similarity=0.156  Sum_probs=66.7

Q ss_pred             cCCeeEecCC--CccC---------CHHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCcc
Q psy15852        183 KSGKIFVGGL--SPEM---------KDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKI  250 (661)
Q Consensus       183 ~~~~lfV~nL--p~~~---------te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~  250 (661)
                      .+++|+|+||  |.++         .++||++.|++||.|..|.+..+    ..+|+|||+|.+.++|.+|+..+ +..+
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            3578999999  5543         23689999999999999998764    45899999999999999999997 6899


Q ss_pred             CCeEEEEEeccCCC
Q psy15852        251 NDKEVDVKKATPKP  264 (661)
Q Consensus       251 ~g~~i~V~~a~~k~  264 (661)
                      +||+|.|.++.++.
T Consensus        83 ~gr~i~v~~~~g~~   96 (99)
T d2dita1          83 GGRQITAQAWDGTT   96 (99)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCEEEEEEEeCCcC
Confidence            99999999987765

>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=98.95  E-value=6.6e-10  Score=91.96  Aligned_cols=63  Identities=22%  Similarity=0.380  Sum_probs=56.9

Q ss_pred             HHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhhcc
Q psy15852        113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKAK  183 (661)
Q Consensus       113 e~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~~~  183 (661)
                      +++|++.|++||+|.+|++..+    +.+|||||+|.++++|.+|    +..+|+..+.|++|.|.++.++
T Consensus        33 ~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A----~~~lng~~~~gr~i~v~~~~g~   95 (99)
T d2dita1          33 REDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYC----IQTLDGRWFGGRQITAQAWDGT   95 (99)
T ss_dssp             HHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHH----HHHSTTCEETTEECEEEECCSC
T ss_pred             HHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHH----HHHhCCcEECCEEEEEEEeCCc
Confidence            3789999999999999998764    4679999999999999999    9999999999999999887654

>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=98.93  E-value=7e-10  Score=92.76  Aligned_cols=80  Identities=14%  Similarity=0.220  Sum_probs=67.1

Q ss_pred             cCCeeEecCC--CccC--------CHHHHHHHHhcCCCeEEEEeccCCCC--CCcCcEEEEEeCCHHHHHHHHHhC-CCc
Q psy15852        183 KSGKIFVGGL--SPEM--------KDEEIKAHFAQFGNIIETEMPYDKSK--SQRKNFCFITFEHESVVIDLLKNP-KQK  249 (661)
Q Consensus       183 ~~~~lfV~nL--p~~~--------te~~L~~~F~~~G~i~~v~i~~~~~~--g~~~g~afV~f~~~~~A~~Al~~~-~~~  249 (661)
                      +++.|.|+|+  |..+        ..+||++.|++||.|.+|.|+++..+  ....|++||+|.+.++|.+|+..+ +..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4678999999  4432        34689999999999999999886654  344689999999999999999987 789


Q ss_pred             cCCeEEEEEeccC
Q psy15852        250 INDKEVDVKKATP  262 (661)
Q Consensus       250 ~~g~~i~V~~a~~  262 (661)
                      ++||.|.+.++.+
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999864

>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=98.86  E-value=1.2e-09  Score=86.48  Aligned_cols=70  Identities=14%  Similarity=0.190  Sum_probs=55.5

Q ss_pred             cEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeeccee-ehhhh
Q psy15852        101 KMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK-IEAKK  179 (661)
Q Consensus       101 ~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~-i~v~~  179 (661)
                      .+++.+++|+++++.| ++|++||+|.++++.+      ++|||||+|.++++|++|    + .+|+..+.|+. |.|.+
T Consensus         6 wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~A----l-~~nG~~~~g~~~vgV~~   73 (81)
T d1wwha1           6 WVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKA----L-SKDGRIFGESIMIGVKP   73 (81)
T ss_dssp             EEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHH----H-TTTTCEETTTEECEEEE
T ss_pred             EEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHH----H-hcCCCeECCcEEEEEEe
Confidence            4666777778876555 6899999999998754      468999999999999997    5 69999999985 44665


Q ss_pred             hhc
Q psy15852        180 AKA  182 (661)
Q Consensus       180 ~~~  182 (661)
                      +..
T Consensus        74 ~~~   76 (81)
T d1wwha1          74 CID   76 (81)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=98.82  E-value=1.1e-09  Score=91.56  Aligned_cols=67  Identities=19%  Similarity=0.314  Sum_probs=58.7

Q ss_pred             CHHHHHHHhhcCCCeeEEEEeeCCCCC--CcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhhhc
Q psy15852        112 ITEELKEHFSKYGEIENVTLKSDPNTG--RSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKAKA  182 (661)
Q Consensus       112 te~~L~~~F~~~G~I~~v~l~~~~~tg--~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~~~  182 (661)
                      ..+||++.|++||.|.+|.|++++.+.  ..+|++||+|.+.++|.+|    +..++|..+.||.|.+.++.+
T Consensus        27 i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A----~~~l~Gr~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          27 IVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKA----MQGLTGRKFANRVVVTKYCDP   95 (104)
T ss_dssp             HHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHH----HHHHSSCCSSSSCCEEEEECH
T ss_pred             HHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHH----HHHHCCCEECCeEEEEEEcCH
Confidence            456899999999999999999876543  4679999999999999999    999999999999999877643

>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=96.28  E-value=0.0072  Score=47.10  Aligned_cols=69  Identities=20%  Similarity=0.116  Sum_probs=55.5

Q ss_pred             CcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCC--cccEEEEEEeehhhHHHhhHHHHHHhCCeeecc
Q psy15852        100 NKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGR--SRGFAFIVFKDTESLEKASVEDVIAEGNHVINN  172 (661)
Q Consensus       100 ~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~--srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g  172 (661)
                      .|+++..|||.+||+++.+.++..|++........+.+-+  .-.-|||.|.+.++...-    ....+++.+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F----~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILF----RDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHH----HHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHH----HHHcCCcEEEc
Confidence            3788999999999999999999999988877776554322  123599999999999886    77888888754

>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=95.86  E-value=0.0046  Score=47.40  Aligned_cols=55  Identities=15%  Similarity=0.346  Sum_probs=48.6

Q ss_pred             HHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhCCCccCCeEEEEEecc
Q psy15852        199 EEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT  261 (661)
Q Consensus       199 ~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~~~~~~g~~i~V~~a~  261 (661)
                      .+|.+.|..||+|.-|++..+        -..|+|.+-++|.+|+...+.++.|+.|.|....
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEETTEEEEEECCC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEEcceEEEEecCC
Confidence            478889999999999999754        4899999999999999999999999999997643

>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=95.80  E-value=0.014  Score=45.40  Aligned_cols=61  Identities=21%  Similarity=0.173  Sum_probs=50.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCc--ccEEEEEEcCHHHHHHHHHh
Q psy15852        594 NKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRS--RGFAFIVFKDTESLEKASVE  654 (661)
Q Consensus       594 ~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s--~G~aFV~F~~~e~A~~A~~~  654 (661)
                      +||.||+||+..||+++.+.+++.|.+....-...+.+-..  ---|+|.|.+.++...-.+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~   64 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDR   64 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHH
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHH
Confidence            68999999999999999999999999998877765443221  14699999999998776664

>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=95.54  E-value=0.014  Score=42.39  Aligned_cols=60  Identities=23%  Similarity=0.258  Sum_probs=51.2

Q ss_pred             HHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       114 ~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      +-|...|+++|+|.++.|....+ +..  .|-|...+..+|..|    +..++...|+.++|.|..+
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~d-g~~--~A~V~v~~~q~A~~~----v~~LhR~KiG~KRI~Vs~~   70 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTD-YQL--KAVVQMENLQDAIGA----VNSLHRYKIGSKKILVSLA   70 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS-TTC--CEEEEESSHHHHHHH----HHHHTTEEETTEEEEEEEC
T ss_pred             HHHHHHHHhheeEEEEEEEeccC-CcE--EEEEEcCCHHHHHHH----HHHHHHHhcCCeEEEEEEe
Confidence            44677899999999999987543 555  599999999999999    9999999999999988654

>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=95.47  E-value=0.0053  Score=47.05  Aligned_cols=55  Identities=18%  Similarity=0.332  Sum_probs=48.3

Q ss_pred             HHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHhhHHHHHHhCCeeecceeehhhhh
Q psy15852        113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKKA  180 (661)
Q Consensus       113 e~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A~~~~~~~~~~~~i~g~~i~v~~~  180 (661)
                      -.+|.+.|..||+|.-||++.+        -..|+|.+-++|.+     ++.+++..+.|+.|.+...
T Consensus        38 ~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~-----al~l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          38 RTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALS-----VLDVDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHH-----HHHGGGSEETTEEEEEECC
T ss_pred             HHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHH-----HhccCCeEEcceEEEEecC
Confidence            3578899999999999999986        58999999999999     6899999999999987543

>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=95.33  E-value=0.022  Score=41.37  Aligned_cols=61  Identities=20%  Similarity=0.266  Sum_probs=50.8

Q ss_pred             HHHHHHHHhcCCCeEEEEeccCCCCCCcCcEEEEEeCCHHHHHHHHHhC-CCccCCeEEEEEecc
Q psy15852        198 DEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP-KQKINDKEVDVKKAT  261 (661)
Q Consensus       198 e~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~~-~~~~~g~~i~V~~a~  261 (661)
                      .+-|.+.|++++.|.++.+....+ +  .-.|-|...+.++|.-|+..+ ..++++++|.|.++.
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~~d-g--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPHTD-Y--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSCCS-T--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHHhheeEEEEEEEeccC-C--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            345667889999999999976543 2  445999999999999999998 579999999999875

>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=94.73  E-value=0.021  Score=44.50  Aligned_cols=52  Identities=21%  Similarity=0.310  Sum_probs=44.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHH
Q psy15852        594 NKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASV  653 (661)
Q Consensus       594 ~~l~v~nlp~~~te~dL~~~F~~~G~I~~v~i~~d~~tg~s~G~aFV~F~~~e~A~~A~~  653 (661)
                      .-+|.-..|-+|...||.++|++||.| .|.-+-|-       -|||.-.+.++|..++.
T Consensus        16 dHVf~~tFP~~Wk~~dI~~lFSpfG~V-~VswIddT-------Sa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          16 DHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHH
T ss_pred             ceeEEEeCCcccchhHHHHHhcCCCce-EEEEecCc-------eEEEEecCHHHHHHHHH
Confidence            458999999999999999999999999 55555442       69999999999988876

>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=90.68  E-value=0.24  Score=38.34  Aligned_cols=52  Identities=23%  Similarity=0.346  Sum_probs=41.7

Q ss_pred             CCCcEEEEcCCCcCCHHHHHHHhhcCCCeeEEEEeeCCCCCCcccEEEEEEeehhhHHHh
Q psy15852         98 AKNKMVSHPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA  157 (661)
Q Consensus        98 ~~~~~~~~~~~~~~te~~L~~~F~~~G~I~~v~l~~~~~tg~srG~afV~F~~~e~A~~A  157 (661)
                      ..+-+|++.-|..+...||.++|+.||.| .|-.+-+  |     .|||...+.++|+.+
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V-~VswIdd--T-----Sa~V~L~~~e~~~~v   65 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDD--T-----SAFVSLSQPEQVQIA   65 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEET--T-----EEEEECSCHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCce-EEEEecC--c-----eEEEEecCHHHHHHH
Confidence            34557777777799999999999999998 3455544  2     699999999999886